gebhart/patrepeval huggingface dataset:
Spatial transcriptomics reveal pitfalls and opportunities for the detection of rare high-plasticity breast cancer subtypes (2023)

Abstract Breast cancer is one of the most prominent types of cancers, in which therapeutic resistance is still a major clinical hurdle. Specific subtypes like Claudin-low (CL) and metaplastic breast cancers (MpBC) have been associated with high non-genetic plasticity, which can facilitate resistance. The overlaps and differences between these orthogonal subtypes, respectively identified by molecular and histopathological analyses, are however still insufficiently characterised. Adequate methods to identify high-plasticity tumours to better anticipate resistance are furthermore still lacking. Here we analysed 11 triple negative breast tumours, including 3 CL and 4 MpBC samples, via high-resolution spatial transcriptomics. We combined pathological annotations and deconvolution approaches to precisely identify tumour spots, on which we performed signature enrichment, differential expression and copy-number analyses. We used the TCGA and CCLE public databases for external validation of expression markers. By levying spatial transcriptomics to focus analyses only to tumour cells in MpBC samples, and therefore bypassing the negative impact of stromal contamination, we could identify specific markers that are not expressed in other subtypes nor stromal cells. Three markers ( BMPER, POPDC3 and SH3RF3 ) could furthermore be validated in external expression databases encompassing bulk tumour material and stroma-free cell lines. We find that existing bulk expression signatures of high-plasticity breast cancers are relevant in mesenchymal transdifferentiated compartments but can be hindered by stromal cell prevalence in tumour samples, negatively impacting their clinical applicability. Spatial transcriptomics analyses can however help identify more specific expression markers, and could thus enhance diagnosis and clinical care of rare high-plasticity breast cancers.
Mechanism of chiral recognition in the enantioseparation of 2‐aryloxypropionic acids on new brush‐type chiral stationary phases (2001)

New brush-type chiral stationary phases (CSP I-IV) comprising N-3,5,6-trichloro-2,4-dicyanophenyl-L-alpha-amino acids (1-4) were prepared by binding of chiral selectors 1-4 to gamma-aminopropyl silica gel. To check the role of excess free aminopropyl groups, CSP V was prepared by binding N-3,5,6-trichloro-2,4-dicyanophenyl-L-alanyl-(3-triethoxysilyl)propylamide to unmodified silica gel. The best separation of racemic 2-aryloxypropionic acids (TR-1-13) was obtained with CSP I; the -(-)-S enantiomer were regularly eluted first, as determined by a CD detector. The mechanism of chiral recognition implies a synergistic interaction of carboxylic acid analyte with the chiral selector and achiral free gamma-aminopropyl units on silica. In fact, CSP V, which is lacking an achiral aminopropyl spacer, shows a lower separation ability for 2-aryloxypropionic acids, but a similar enantioselective discrimination of esters TR-19-20, in comparison with CSP I. CSP I-IV retain unaltered separation ability after a few months of continuous work using a large number of various mobile phases.
Improving Security Visualization with Exposure Map Filtering (2008)

Graphical analysis of network traffic flows helps security analysts detect patterns or behaviors that would not be obvious in a text-based environment. The growing volume of network data generated and captured makes it increasingly difficult to detect increasingly sophisticated reconnaissance and stealthy network attacks. We propose a network flow filtering mechanism that leverages the exposure maps technique of Whyte et al. (2007), reducing the traffic for the visualization process according to the network services being offered. This allows focus to be limited to selected subsets of the network traffic, for example what might be categorized (correctly or otherwise) as the unexpected or potentially malicious portion. In particular, we use this technique to filter out traffic from sources that have not gained knowledge from the network in question. We evaluate the benefits of our technique on different visualizations of network flows. Our analysis shows a significant decrease in the volume of network traffic that is to be visualized, resulting in visible patterns and insights not previously apparent.
Analysing EHR navigation patterns and digital workflows among physicians during ICU pre-rounds (2020)

From the study findings, we suggest recommendations towards improved EHR design.
Synthesis and Evaluation of Analogues of the Partial Agonist 6-(Propyloxy)-4-(methoxymethyl)-β-carboline-3-carboxylic Acid Ethyl Ester (6-PBC) and the Full Agonist 6-(Benzyloxy)-4-(methoxymethyl)-β- carboline-3-carboxylic Acid Ethyl Ester (Zk 93423) at Wild Type and Recombinant GABAA Receptors (1998)

A pharmacophore and an alignment rule have previously been reported for BzR agonist ligands. The design and synthesis of 6-(propyloxy)-4-(methoxymethyl)-beta-carboline-3-carboxylic acid ethyl ester (6-PBC, 24, IC50 = 8.1 nM) was based on this pharmacophore. When evaluated in vivo this ligand exhibited anticonvulsant/anxiolytic activity but was devoid of the muscle relaxant/ataxic effects of "classical" 1,4-benzodiazepines (i.e., diazepam). Significantly, 6-PBC 24 also reversed diazepam-induced muscle relaxation in mice. The 3-substituted analogues 40-46 and 48 of 6-PBC 24 and Zk 93423 27(IC50 = 1 nM) were synthesized and evaluated in vitro to determine what affect these modifications would have on the binding affinity at recombinant BzR subtypes. With the exception of the 3-amino ligands 40 and 41, all the beta-carbolines were found to exhibit high binding affinity at BzR sites. The 3-propyl ether derivative 45 was also evaluated in vivo and found to be devoid of any proconvulsant or anticonvulsant activity at doses up to 40 mg/kg. The 6-(1-naphthylmethyloxy) and 6-octyloxy analogues 25, 26, 28, and 29 of 6-PBC 24 were synthesized to further evaluate the proposed alignment of agonists vs inverse agonists in the pharmacophore of the BzR. In addition, ligands 26 and 29 were designed to probe the dimensions of lipophilic pocket L3 at the agonist site. The activity of 29 was evaluated in vivo; however, this analogue elicited no pharmacological effects at doses up to 80 mg/kg. These and other related beta-carbolines were also examined in five recombinant GABAA receptor subtypes. Ligands 52-61 all exhibited moderate to high affinity at GABAA receptors containing alpha1 subunits. These ligands will be useful in further defining the pharmacophore at alpha1 beta3 gamma2 receptors.
A novel 3D multispectral vision system based on filter wheel cameras (2016)

The combination of the multispectral imaging and the 3D imaging in one system would render possible varieties of applications in different fields. In this work a method is proposed for the registration of multispectral data and 3D point cloud, in which the number of spectral bands is increased by combining different multispectral images through 3D information. Based on this method, a 3D multispectral imaging system consisting of two filter wheel cameras and a digital projector is developed. This system can provide maximally 23 spectral bands with a short acquisition duration of ca. 1.5 seconds and achieve a data fusion accuracy of 15 μm for a measurement field of 128 mm × 145 mm. Furthermore, there exists a significant potential to extend the spectral range and raise the spectral resolution by integrating additional cameras with the proposed data fusion principle.
A π/4-shift Qpsk Receiver For Tdma/tdd Systems (2005)

This paper proposes a n Mshij? QPSK receiver for microcellular TDMMDD systems. The receiver is suited for an all digital implementation. It assumes a coarse automatic gain-control (AGC), which is updated digitally. The receiver uses a new maximumlikelihood (ML) based scheme for fast synchronization in its all-digital timing recovery circuit. The proposed timing acquisition scheme is independent of the AGC setting and does not suffer from hangups..
Automated seeded lesion segmentation on digital mammograms (1998)

Segmenting lesions is a vital step in many computerized mass-detection schemes for digital (or digitized) mammograms. We have developed two novel lesion segmentation techniques-one based on a single feature called the radial gradient index (RGI) and one based on simple probabilistic models to segment mass lesions, or other similar nodular structures, from surrounding background. In both methods a series of image partitions is created using gray-level information as well as prior knowledge of the shape of typical mass lesions. With the former method the partition that maximizes the RGI is selected. In the latter method, probability distributions for gray-levels inside and outside the partitions are estimated, and subsequently used to determine the probability that the image occurred for each given partition. The partition that maximizes this probability is selected as the final lesion partition (contour). We tested these methods against a conventional region growing algorithm using a database of biopsy-proven, malignant lesions and found that the new lesion segmentation algorithms more closely match radiologists' outlines of these lesions. At an overlap threshold of 0.30, gray level region growing correctly delineates 62% of the lesions in our database while the RGI and probabilistic segmentation algorithms correctly segment 92% and 96% of the lesions, respectively.
Irregular Motion Detection in Automotive Navigation Systems with Soft Map Rotation (2019)

Visually unpleasant and erroneous positioning in navigation scenes is an issue for, but not limited to, premium vehicle manufacturers. In order to assure consumers high quality products, intelligent automated display testing is required. This paper presents an enhanced version of an error detection algorithm for navigation sequences based on novelty detection. Therefore, motion parameters obtained from real world navigation sequences are used. These are taken directly from the display using a screen-grabbing device. The proposed algorithm works solely on the information provided in these images. Several image processing methods extract information describing the overall motion between two consecutive frames which is then fed into a novelty detection algorithm to predict outliers. In this case, these outliers describe motions that should not occur in the displayed scene as they display impossible movements of the car. Experimental results demonstrate the improvement over the state of the art, being able to deal with recent changes in the displayed scene in order to hide or conceal present positioning errors. Evaluating the performance of the proposed algorithm, a precision of 76.2%, which is significantly higher than the state of the art method, could be reached while not decreasing the recall at all.
Coaxially Stacked RNA Helices in the Catalytic Center of the Tetrahymena Ribozyme (1994)

Coaxial stacking of helical elements is a determinant of three-dimensional structure in RNA. In the catalytic center of the Tetrahymena group I intron, helices P4 and P6 are part of a tertiary structural domain that folds independently of the remainder of the intron. When P4 and P6 were fused with a phosphodiester linkage, the resulting RNA retained the detailed tertiary interactions characteristic of the native P4-P6 domain and even required lower magnesium ion concentrations for folding. These results indicate that P4 and P6 are coaxial in the P4-P6 domain and, therefore, in the native ribozyme. Helix fusion could provide a general method for identifying pairs of coaxially stacked helices in biological RNA molecules.
Prevalence and Mechanism of Fluoroquinolone Resistance in Escherichia coli Isolated from Swine Feces in Korea (2017)

In this study, we investigated the prevalence and fluoroquinolone (FQ) resistance mechanisms in Escherichia coli isolated from swine fecal samples. E. coli isolates were collected from 171 (72.2%) of 237 swine fecal samples. Of these, 59 isolates (34.5%) were confirmed as FQ-resistant E. coli by the disk diffusion method. Of the FQ-resistant isolates, three major FQ resistance mechanisms were investigated. Of the 59 isolates, plasmid-mediated quinolone resistance genes were detected in 9 isolates (15.3%). Efflux pump activity was found in 56 isolates (94.9%); however, this was not correlated with the increased FQ resistance measured by determining the MIC. Point mutations in quinolone resistance-determining regions were the main cause of FQ resistance. All 59 ciprofloxacin-resistant isolates had mutations in quinolone resistance-determining regions; of these 59 isolates, all (100%) had mutations in gyrA, 58 (98.3%) had mutations in parC, 22 (37.3%) had mutations in parE, and none had mutations in gyrB. The predominant mutation type was double mutation in gyrA (Ser83Leu plus mutation in aspartic acid 87), and all FQ-resistant isolates (except one) that had mutations in parC or parE also had double mutations in gyrA. Importantly, the frequencies of multidrug-resistant and extended-spectrum β-lactamase-producing E. coli were significantly higher in the high ciprofloxacin MIC group in this study. Compared with previous studies in Korea, the prevalence of FQ resistance and plasmid-mediated quinolone resistance genes had increased considerably in swine. Although the use of FQ as a feed additive is prohibited in Korea, use for self-treatment and therapeutic purposes has been increasing, which may be responsible for the higher FQ resistance rate observed in this study. Therefore, prudent use of FQ on animal farms is warranted to reduce the evolution of FQ-resistant bacteria in the animal industry.
Language abstractions and program analysis techniques to build reliable, efficient and robust networked systems (2010)

Networked systems have an important role in our lives. Ranging from the Internet to new and upcoming domains like wireless sensor networks, smart-phones and data-centers, they are transforming the way we use computing. For networked systems to be of practical use, they need to be reliable, efficient , and robust. Building such systems poses a number of programming challenges.
In this dissertation, we show that it is possible to adapt analysis and design techniques from the programming languages community and combine them with domain knowledge and simple user insights to address the programming challenges for specific network domains.
We present tools and techniques to simplify the task of building reliable, efficient, and robust networked systems for the domains of wireless sensor networks and network protocols. We introduce Pleiades, a centralized programming framework for wireless sensor networks. We present FSMGen, a tool for wireless sensor networks, that automatically derives user-understandable and compact finite state machines from TinyOS programs. We also describe MAX, a tool that explores network protocol implementations written in C for vulnerability to manipulation attacks.
These tools and systems address various programming challenges faced by developers of wireless sensor networks and network protocols. We demonstrate their utility and benefits via detailed evaluation and experiments under realistic conditions.
A Novel Energy-Efficient Training Method for Receive Antenna Selection (2010)

Receive antenna selection (AS), in which only a subset of antennas receive simultaneously at any time, requires the transmitter to send pilots multiple times so that the receiver can acquire channel state of all antennas and select the best subset. In conventional AS training, sensitivity of coherent reception to channel estimation errors forces the transmitter to boost the energy allocated to all pilots to ensure accurate channel estimates. Energy for pilots received by unselected antennas is mostly wasted, especially since the selection process is robust to estimation errors. In this paper, we propose a novel training method uniquely tailored for AS. Using one extra pilot symbol, accurate channel estimates get generated for the antenna subset that actually receives data. Consequently, the transmitter can selectively boost the energy allocated to the extra pilot. Other pilots, which now primarily help in subset selection, get allocated less energy. We derive closed-form expressions for the proposed scheme's symbol error probability, and optimize the energy allocated to pilot and data symbols. We show that the optimal solution achieves full diversity; it is provably unique and strictly better than the conventional model.
Using micro-RNA expression to predict response to neoadjuvant chemotherapy in urothelial carcinoma of the bladder. (2013)

299 Background: Urothelial carcinoma of the bladder is among the 5 most common cancers in the US. Despite several clinical trials attempting to determine the best approach to muscle-invasive disease, the optimal treatment modalities and their sequence have not been established. Specifically, the decision to administer neo-adjuvant chemotherapy is currently based solely on clinical parameters, with no validated biomarkers. Micro-RNAs (miRNAs) are short RNA molecules that have roles in post-transcriptional gene expression regulation by binding to mRNAs. They were shown to have cardinal roles in many cancers, and their potential to serve as biomarkers is extensively studied. Our goal was to study whether miRNAs can serve as predictive biomarkers for response to neo-adjuvant chemotherapy in urothelial carcinoma. Methods: miRNAs were extracted from paraffin-embedded pre-operative muscle-invasive tumor biopsies of patients diagnosed with urothelial carcinoma, whose pathological surgical specimen was later found to either show complete or no-response to neo-adjuvant chemotherapy (termed 'responders' and 'non-responders', respectively). The expression pattern of approximately 900 miRNAs was compared using a commercial miRNA array, and the levels of candidate miRNAs was further assessed by quantitative real-time PCR (qRT-PCR). Results: The vast majority of miRNAs exhibited a similar expression pattern in the two patient groups, but two miRNAs were significantly lower in the responders (p &lt;0.001 and q&lt;0.1 using the false detection rate (FDR) method). Interestingly, both miRNAs can potentially target the mRNA of PTCH1 and SP5, two genes with known tumor-suppressor functions. qRT-PCR showed that high levels of one of the miRNAs correlated with lack of response to chemotherapy. Conclusions: This retrospective analysis identified two miRNAs that are differentially expressed between chemotherapy responders and non-responders. One of these miRNAs was confirmed to correlate with lack of response to neo-adjuvant chemotherapy. A prospective trial assessing the predictive values of these miRNAs is currently underway. Future research directions and potential implications will be discussed.
ChemInform Abstract: Regioselective Transformation of Alkynes into Cyclic Acetals and Thioacetals with a Gold(I) Catalyst: Comparison with Broensted Acid Catalysts. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.
Cholesterol oxidase: an oöstatic and larvicidal agent active against the cotton boll weevil, Anthonomus grandis (1995)

Abstract The enzyme cholesterol oxidase (E.C. 1.1.3.6), purified from Streptomyces culture filtrate was previously found to have oral insecticidal activity on neonate larvae of the boll weevil ( Anthonomus grandis grandis Boheman) from a laboratory population. In the present study, second instar larvae were also controlled by the enzyme at diet concentrations similar to those which control neonates (12 day LC 50 = 2.4 μg.ml −1 in diet). Larvae from field‐collected adults were similarly susceptible to cholesterol oxidase in the diet. When ingested by adult females during the mating/pre‐oviposition period, cholesterol oxidase greatly reduced subsequent oviposition (83% reduction in eggs laid as compared to controls) and larval survival (97% reduction from controls). Dissection of treated adult females revealed poorly developed ovaries and few developing oöcytes. These studies were conducted to further evaluate the utility of cholesterol oxidase in a program to establish boll weevil‐resistant transgenic cotton.
Influence of double Rayleigh backscattering on Raman amplified higher order modulation transmissions (2017)

State-of-the-art optical transponders use a coherent detection scheme with higher order modulation formats to achieve bitrates as high as 400 Gbit/s. However, the use of higher order modulation formats, like 16-QAM, increases the requirements on the optical signal-to-noise ratio (OSNR) [1]. To utilize even higher order modulation formats, e.g. 64-QAM, noise in the transmission system must be minimized. Distributed Raman amplifiers can be used to achieve low noise amplification [1], but introduce a new kind of noise: multi path interference (MPI) by double Rayleigh backscattering (DRB). This limits the practically useable gain [1]. To study the still unknown influence of DRB on higher order modulation we numerically simulate a contra directional pumped distributed Raman amplifier. As in [2] the Raman amplifier is modelled as a set of coupled differential equations. The resulting boundary value problem is solved with a fourth-order Runge-Kutta method [3]. The model provides the powers of all signal, pump and noise terms in the system. Hence, a system OSNR is calculated, covering forward amplified spontaneous emission (ASE) and DRB. Afterwards, a third term describing imperfect electrical components is introduced to the calculation. To compare the simulation results with experimental results the system OSNR is converted to an error vector magnitude (EVM).
DeltaMotion Hip System - Two Year Outcomes (2013)

Introduction The Delta Motion device (developed by Finsbury Orthopaedics, Leatherhead, United Kingdom, now manufactured by DePuy, Leeds, United Kingdom) is a pre-assembled factory fitted cup. It has been introduced to overcome some of the concerns relating to intra-operative assembly with improper seating of the liner and chipping. This device has a thinner shell and liner in comparison with other cups, allowing the use of larger sized heads which should help reduce the risk of impingement and dislocation. A drawback of the pre-assembled design is the inability to use supplementary screws to achieve stability and the difficulty in obtaining primary stability compared with a thin titanium shell. To date we are not aware of any publications reviewing the outcomes of these devices. Methods 206 DeltaMotion cups were implanted in 195 patients, between Dec 2008 to Dec 2009 by the three senior authors. All the hips had the same stem (Osteonics) and a ceramic head was used. Data was prospectively collected and we reflect on our two year results. Results A total of 206 cups (123 F: 83 M) were implanted in 195 patients. The mean age at implantation was 69 years (range 38–93). 11 patients had bilateral hips (6M:5F). Complications were 1 pulmonary embolism, 2 femoral stem subsidence, 1 dislocation, 2 femoral fractures, 13 squeaking hips (9F:4M). The squeaking hips had a mean age of 65 years. Discussion The main complication was ‘benign’ squeaking. This was more common in younger (mean age 64 years) females. This cohort has a squeaking rate of 6.3% which is higher than 3.1% previously reported by our unit. There was no squeaking when 36 mm heads were used. The risk of squeaking dramatically increased when cup sizes 60 mm and above were used with 48 mm heads. Although squeaking seems to have increased with this device, none of the patients required revision.