gebhart/patrepeval huggingface dataset:
Sorting with linear speedup on a pipelined hypercube (1992)

The authors formally define a distributed-memory parallel architecture called the pipelined hypercube. A coarse-grained parallel sorting algorithm that can be mapped efficiently on such an architecture is also presented. The pipelined hypercube has a more powerful communication mechanism than the traditional binary code architecture, in that it permits communication of blocks of data between processing elements (PEs) to be performed in a pipelined manner. Certain data communication problems which would probably be serialized on the binary code architecture, can be performed optimally on the pipelined hypercube. The sorting algorithm can be mapped efficiently onto a pipelined hypercube of P PEs. It sorts N data items, initially distributed among the PEs, in time O((N log N/P)+log/sup 2/ P), thereby achieving linear speedup when P is O(N/log N).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A Fully Integrated Continuous‐Flow System for Asymmetric Catalysis: Enantioselective Hydrogenation with Supported Ionic Liquid Phase Catalysts Using Supercritical CO2 as the Mobile Phase (2013)

A continuous-flow process based on a chiral transition-metal complex in a supported ionic liquid phase (SILP) with supercritical carbon dioxide (scCO(2)) as the mobile phase is presented for asymmetric catalytic transformations of low-volatility organic substrates at mild reaction temperatures. Enantioselectivity of >99% ee and quantitative conversion were achieved in the hydrogenation of dimethylitaconate for up to 30 h, reaching turnover numbers beyond 100000 for the chiral QUINAPHOS-rhodium complex. By using an automated high-pressure continuous-flow setup, the product was isolated in analytically pure form without the use of any organic co-solvent and with no detectable catalyst leaching. Phase-behaviour studies and high-pressure NMR spectroscopy assisted the localisation of optimum process parameters by quantification of substrate partitioning between the IL and scCO(2). Fundamental insight into the molecular interactions of the metal complex, ionic liquid and the surface of the support in working SILP catalyst materials was gained by means of systematic variations, spectroscopic studies and labelling experiments. In concert, the obtained results provided a rationale for avoiding progressive long-term deactivation. The optimised system reached stable selectivities and productivities that correspond to 0.7 kgL(-1)h(-1) space-time yield and at least 100 kg product per gram of rhodium, thus making such processes attractive for larger-scale application.
Primary Salivary Human Stem/Progenitor Cells Undergo Microenvironment-Driven Acinar-Like Differentiation in Hyaluronate Hydrogel Culture (2016)

Radiotherapy for head and neck cancer often has undesirable effects on salivary glands that lead to xerostomia or severe dry mouth, which can increase oral infections. Our goal is to engineer functional, three-dimensional (3D) salivary gland neotissue for autologous implantation to provide permanent relief. An immediate need exists to obtain autologous adult progenitor cells as the use of embryonic and induced pluripotent stem cells potentially pose serious risks such as teratogenicity and immunogenic rejection. Here, we report an expandable population of primary salivary human stem/progenitor cells (hS/PCs) that can be reproducibly and scalably isolated and propagated from tissue biopsies. These cells have increased expression of progenitor markers (K5, K14, MYC, ETV4, ETV5) compared with differentiation markers of the parotid gland (acinar: MIST1/BHLHA15 and AMY1A; ductal: K19 and TFCP2L1). Isolated hS/PCs grown in suspension formed primary and secondary spheres and could be maintained in long-term 3D hydrogel culture. When grown in a customized 3D modular hyaluronate-based hydrogel system modified with bioactive basement membrane-derived peptides, levels of progenitor markers, indices of proliferation, and viability of hS/PCs were enhanced. When appropriate microenvironmental cues were provided in a controlled manner in 3D, such as stimulation with β-adrenergic and cholinergic agonists, hS/PCs differentiated into an acinar-like lineage, needed for saliva production. We conclude that the stem/progenitor potential of adult hS/PCs isolated without antigenic sorting or clonal expansion in suspension, combined with their ability to differentiate into specialized salivary cell lineages in a human-compatible culture system, makes them ideal for use in 3D bioengineered salivary gland applications. Stem Cells Translational Medicine 2017;6:110-120.
A study on application to gait analysis of joint torque estimation using wearable sensor system (2018)

This paper proposes the estimation method of joint torque in gait analysis using the wearable sensor system installing the inertial sensors and the wearable force plates. In this method, joint torques are calculated by inverse dynamics analysis using the Newton-Euler method, and the joint torques are compensated by using the Unscented Kalman filter and the conditions of the body structure. This method estimates the joint torque compensating the accumulative error by transmission of force and moment in the Newton-Euler method. We conducted the measurement experiment the 5m gait test, and we estimated the compensated joint torques. The results by proposed method showed the same tendency as before the compensation, and the offset error was compensated. This method can be used for the gait analysis using the wearable sensor system.
Data from Association of Inflammation-Related and microRNA Gene Expression with Cancer-Specific Mortality of Colon Adenocarcinoma (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Inflammatory genes and microRNAs have roles in colon carcinogenesis; therefore, they may provide useful biomarkers for colon cancer. This study examines the potential clinical utility of an inflammatory gene expression signature as a prognostic biomarker for colon cancer in addition to previously examined &lt;i&gt;miR-21&lt;/i&gt; expression.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Quantitative reverse transcriptase-PCR. was used to measure the expression of 23 inflammatory genes in colon adenocarcinomas and adjacent noncancerous tissues from 196 patients. These data were used to develop models for cancer-specific mortality on a training cohort (&lt;i&gt;n&lt;/i&gt; = 57), and this model was tested in both a test (&lt;i&gt;n&lt;/i&gt; = 56) and a validation (&lt;i&gt;n&lt;/i&gt; = 83) cohort. Expression data for &lt;i&gt;miR-21&lt;/i&gt; were available for these patients and were compared and combined with inflammatory gene expression.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; &lt;i&gt;PRG1, IL-10, CD68, IL-23a&lt;/i&gt;, and &lt;i&gt;IL-12a&lt;/i&gt; expression in noncancerous tissue, and &lt;i&gt;PRG1, ANXA1, IL-23a, IL-17a, FOXP3&lt;/i&gt;, and &lt;i&gt;HLA-DRA&lt;/i&gt; expression in tumor tissues were associated with poor prognosis based on Cox regression (|Z-score| &gt;1.5) and were used to generate the inflammatory risk score (IRS). IRS was associated with cancer-specific mortality in the training, test (&lt;i&gt;P&lt;/i&gt; = 0.01), and validation (&lt;i&gt;P&lt;/i&gt; = 0.02) cohorts. This association was strong for stage II cases (&lt;i&gt;P&lt;/i&gt; = 0.002). Expression of &lt;i&gt;miR-21&lt;/i&gt; was associated with &lt;i&gt;IL-6, IL-8, IL-10, IL-12a&lt;/i&gt;, and &lt;i&gt;NOS2a&lt;/i&gt;, providing evidence that the function of this microRNA and these inflammatory genes are linked. Both IRS and &lt;i&gt;miR-21&lt;/i&gt; expression were independently associated with cancer-specific mortality, including stage II patients alone.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusion:&lt;/b&gt; IRS and &lt;i&gt;miR-21&lt;/i&gt; expression are independent predictors of colon cancer prognosis and may provide a clinically useful tool to identify high-risk patients. (Clin Cancer Res 2009;15(18):5878–87)&lt;/p&gt;&lt;/div&gt;
C. elegans ORFeome Version 3.1: Increasing the Coverage of ORFeome Resources With Improved Gene Predictions (2004)

The first version of the Caenorhabditis elegans ORFeome cloning project, based on release WS9 of Wormbase (August 1999), provided experimental verifications for ∼55% of predicted protein-encoding open reading frames (ORFs). The remaining 45% of predicted ORFs could not be cloned, possibly as a result of mispredicted gene boundaries. Since the release of WS9, gene predictions have improved continuously. To test the accuracy of evolving predictions, we attempted to PCR-amplify from a highly representative worm cDNA library and Gateway-clone ∼4200 ORFs missed earlier and for which new predictions are available in WS100 (May 2003). In this set we successfully cloned 63% of ORFs with supporting experimental data (“touched” ORFs), and 42% of ORFs with no supporting experimental evidence (“untouched” ORFs). Approximately 2000 full-length ORFs were cloned in-frame, 13% of which were corrected in their exon/intron structure relative to WS100 predictions. In total, ∼12,500 C. elegans ORFs are now available as Gateway Entry clones for various reverse proteomics (ORFeome v3.1). This work illustrates why the cloning of a complete C. elegans ORFeome, and likely the ORFeomes of other multicellular organisms, needs to be an iterative process that requires multiple rounds of experimental validation together with gradually improving gene predictions.
[Low grade pulmonary sarcoma preceding the discovery of a uterine primary]. (2003)

This is the second case of a pulmonary metastasis discovered before a primary low grade uterine sarcoma. The first was found during the investigation of a pulmonary sarcoma. The main differential diagnosis to consider is metastatic leiomyosarcoma. In both cases their finding justifies the search for a uterine primary by immunohistochemical examination for oestrogen and progesterone receptors as well as pelvic ultrasound or even magnetic resonance imaging.
A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2 (2021)

The SARS-CoV-2 pandemic has caused over 1 million deaths globally, mostly due to acute lung injury and acute respiratory distress syndrome, or direct complications resulting in multiple-organ failures. Little is known about the host tissue immune and cellular responses associated with COVID-19 infection, symptoms, and lethality. To address this, we collected tissues from 11 organs during the clinical autopsy of 17 individuals who succumbed to COVID-19, resulting in a tissue bank of approximately 420 specimens. We generated comprehensive cellular maps capturing COVID-19 biology related to patients' demise through single-cell and single-nucleus RNA-Seq of lung, kidney, liver and heart tissues, and further contextualized our findings through spatial RNA profiling of distinct lung regions. We developed a computational framework that incorporates removal of ambient RNA and automated cell type annotation to facilitate comparison with other healthy and diseased tissue atlases. In the lung, we uncovered significantly altered transcriptional programs within the epithelial, immune, and stromal compartments and cell intrinsic changes in multiple cell types relative to lung tissue from healthy controls. We observed evidence of: alveolar type 2 (AT2) differentiation replacing depleted alveolar type 1 (AT1) lung epithelial cells, as previously seen in fibrosis; a concomitant increase in myofibroblasts reflective of defective tissue repair; and, putative TP63<sup>+</sup> intrapulmonary basal-like progenitor (IPBLP) cells, similar to cells identified in H1N1 influenza, that may serve as an emergency cellular reserve for severely damaged alveoli. Together, these findings suggest the activation and failure of multiple avenues for regeneration of the epithelium in these terminal lungs. SARS-CoV-2 RNA reads were enriched in lung mononuclear phagocytic cells and endothelial cells, and these cells expressed distinct host response transcriptional programs. We corroborated the compositional and transcriptional changes in lung tissue through spatial analysis of RNA profiles <i>in situ</i> and distinguished unique tissue host responses between regions with and without viral RNA, and in COVID-19 donor tissues relative to healthy lung. Finally, we analyzed genetic regions implicated in COVID-19 GWAS with transcriptomic data to implicate specific cell types and genes associated with disease severity. Overall, our COVID-19 cell atlas is a foundational dataset to better understand the biological impact of SARS-CoV-2 infection across the human body and empowers the identification of new therapeutic interventions and prevention strategies.
Utilising remote sensing to digitally map discontinuities in tunnelling (2023)

Extracting rock discontinuity parameters from a rock mass using remote sensing equipment, which is increasingly being mounted on remotely operated vehicles, is essential to improve safety, data processing efficiency and data quality. Over the last decade, research has focused on extracting rock discontinuity parameters from point cloud data collected from above-ground environments such as quarries, rock slopes, road cutting, etc. However, the extraction of rock discontinuity parameters from point cloud data via manual digital mapping and, more recently, using semi-automatic algorithms is steadily becoming the new normal. This research focuses on extracting rock discontinuity sets dip and dip direction from point cloud data collected from a drill and blast tunnel section. The approach has identified the limitation of using DSE in hard rock drill and blast tunnels and set the framework for additional research using the DSE and other semi-automatic algorithms in hard rock tunnels to extract rock discontinuity parameters from point clouds.
Spectral Domain Optical Processing Techniques. (1995)

Optical techniques for spectral domain processing (SDP) have been investigated. A computer model for the design of nonlinear devices for frequency mixing in multiquantum well (MQW) materials has been developed. The model has been used to calculate nonlinear coefficients for mixing of pump lasers at wavelengths near 1.3um and 1.55 um to produce and output near 8.05um. A device length for conversion of 0.6 mm is predicted for a pump power density of 106W/ cm2. A quasi-phase-matching scheme for obtaining high conversion efficiency in a dispersive semiconductor material has been devised. An N-dimensional hyper cube network configuration making use of the frequency conversion devices has been propose The scheme allows for all-optical transmission of data from source node to-destination node without optical-to-electrical conversion.
Abstract 5777: EMD 1214063, an exquisitely selective c-Met kinase inhibitor in clinical phase 1 (2010)

Abstract The role of the receptor tyrosin kinase c-Met in tumor progression, metastasis and aggressiveness has been convincingly demonstrated in preclinical and early clinical settings. Several compounds with different selectivity profiles inhibiting c-Met are currently under preclinical/clinical investigation and might emerge as valuable cancer therapeutics in the future. During an HTS run N-(3-(3,6-Dihydro-5-(3,4-dimethoxyphenyl)-2-oxo-2H-1,3,4-thiadiazin-3-ylmethyl)-phenyl)-carbaminic acid-(3-(N,N-diethylamino)-propylester) (1) was identified as an attractive lead structure with an interesting overall profile (clogD (7.4): 2.5, S (pH 7.4): &amp;gt;100 µg/ml, IC50 (c-Met in vitro): 30 nM, IC50 (c-Met cellular): 800 nM) providing a valid starting point for lead optimization. The co-crystal structure of 1 revealed the binding mode and the essential structural features. The initial HTS hit was bound in a DFG-in conformation interacting namely with the main chain nitrogen atom of methionine 1160 within the hinge region and with the main chain nitrogen of aspartic acid 1222. After subsequent optimization of potency, efficacy, PK properties and the safety profile of thiadiazinone 1, EMD1214063 was identified as candidate for further development and is currently investigated in a phase 1 clinical trial. The pyridazinone EMD1214063 inhibits enzymatic and cellular c-Met kinase activity with IC50 values in the low nanomolar range. This compound displayed an exquisite selectivity when tested in vitro against a panel of more than 250 potential off-targets, including kinases, GPCRs, ion channels, transporters and various enzymes and demonstrated excellent anti-tumor activity in vivo in a variety of xenograft models. Depending on the particular model, complete regressions were observed with doses as low as 6 mg/kg/d administered per os. The overall profile of EMD1214063 including first time disclosure of the precise structure, synthesis, structure activity relationships, in vitro potency, selectivity profile, pharmacokinetic and in vivo data will be discussed. Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 5777.
Extended many-body superradiance in diamond epsilon near-zero metamaterials (2022)

We theoretically and numerically demonstrate enhanced extended superradiance using a diamond epsilon near-zero metamaterial design. Due to the large spatial coherence in this metamaterial, we experience an ultra-high superradiant decay rate enhancement over distances greater than 13 times the free-space wavelength for both two emitters and many-body configurations of emitters. We observe a power enhancement three orders of magnitude higher than an incoherent array of emitters in bulk diamond, corresponding to an N2 scaling with the number of emitters characteristic of superradiance.
High-Harmonic Synchronization of Optomechanical Oscillators (2020)

We experimentally demonstrate injection locking of an optomechanical oscillator driven at multiple harmonics of its fundamental frequency. The measured Arnold tongues show strongest synchronization when driven at even harmonics.
Induction of Specific Cytotoxic Lymphocytes in Mice Vaccinated withBrucella abortusRB51 (2001)

A safe, more sensitive, nonradioactive, neutral red uptake assay was adopted to replace the traditional 51Cr release assay for detection of Brucella-specific cytotoxic T lymphocyte (CTL) activity. Our studies indicated that Brucella abortus strain RB51 vaccination of mice induced specific CTLs against both strain RB51- and strain 2308-infected J774.A1 macrophages but not against Listeria monocytogenes-infected J774.A1 cells. The antigen-specific cytotoxic activity was exerted by T lymphocytes but not by NK cells. CD3+ CD4+ T cells secreted the highest level of gamma interferon (IFN-gamma) and were able to exert a low but significant level of specific lysis of Brucella-infected macrophages. They also exerted a low level of nonspecific lysis of noninfected macrophages. In contrast, CD3+ CD8+ T cells secreted low levels of IFN-gamma but demonstrated high levels of specific lysis of Brucella-infected macrophages with no nonspecific lysis. These findings indicate that B. abortus strain RB51 vaccination of mice induces specific CTLs and suggest that CD3+ CD4+ and CD3+ CD8+ T cells play a synergistic role in the anti-Brucella activity.
Contract Specification for Hardware Interoperability Testing and Fault Analysis (2011)

Hardware failures occur especially due to external influences, component aging, or faulty interoperability. By testing, faulty components can be localized, allowing for fault isolation or repair. The contract testing strategy from software specifies component interoperability conditions, and systematically creates correspondent tests ensuring the operability of the system. We adapt contract testing to hardware, providing component specification, and monitoring thereof. Contract specification has to be specialized with requirements on the physical environment and component input signals. Contract testing is then executed through the monitoring of the contract parameters. Furthermore, to reason about the external cause of errors, signal faults are categorized. As a case study, we present an communication system. For this system, a contract is defined, and circuits implemented to perform contract testing and fault categorization. Communication faults, related to hardware errors and to sporadic environment disturbance, are injected in the developed system. These faults are completely detected, but can be only partially categorized by the monitoring approach.
Power-Efficient Decision-Feedback Equalizers for Multi-Gb/s CMOS Serial Links (2007)

A decision-feedback equalizer (DFE) can compensate for severe signal distortion due to limited channel bandwidth, but its typical power consumption is too high for some applications. This paper describes three CMOS DFEs which embody different design techniques for improved power efficiency. The first one, with two taps, uses a soft decision technique to reduce the critical path delay of the first feedback tap, so that the analog summers can be operated at low currents. This DFE consumes 4.8 mW at 6 Gb/s. The second one, with one tap, employs speculation to relax the critical timing. Speculation increases the number of parallel data paths, but the power dissipation of each path is kept low by using a single switched-capacitor circuit for both sampling and DFE summation. This DFE consumes 5.0 mW at 6 Gb/s. The third one, with two taps, also employs speculation. High power efficiency (9.3 mW at 7 Gb/s) is achieved by implementing the analog summers as resettable integrators.
Ergodic Capacity Analysis of AF DH MIMO Relay Systems With Residual Transceiver Hardware Impairments: Conventional and Large System Limits (2017)

Despite the inevitable presence of transceiver impairments, most prior work on multiple-input multiple-output (MIMO) wireless systems assumes perfect transceiver hardware, which is unrealistic in practice. In this direction, motivated by the increasing interest in MIMO relay systems due to their improved spectral efficiency and coverage, this paper investigates the impact of residual hardware impairments on the ergodic capacity of dual-hop (DH) amplify-and-forward (AF) MIMO relay systems. Specifically, a thorough characterization of the ergodic channel capacity of DH AF relay systems in the presence of hardware impairments is presented herein for both the finite and large antenna regimes by employing results from finite-dimensional and large random matrix theory, respectively. Regarding the former setting, we derive the exact ergodic capacity as well as closed-form expressions for tight upper and lower bounds. Furthermore, we provide an insightful study for the low signal-to-noise ratio regimes. Next, the application of the free probability theory allows us to study the effects of the hardware impairments in future 5G deployments including a large number of antennas. While these results are obtained for the large system limit, simulations show that the asymptotic results are quite precise even for conventional system dimensions.
Supplementary Tables 1-2, Figures 1-2, Material and Methods from Formation of the eIF4F Translation–Initiation Complex Determines Sensitivity to Anticancer Drugs Targeting the EGFR and HER2 Receptors (2023)

Supplementary Tables 1-2, Figures 1-2, Material and Methods from Formation of the eIF4F Translation–Initiation Complex Determines Sensitivity to Anticancer Drugs Targeting the EGFR and HER2 Receptors