gebhart/patrepeval huggingface dataset:
Positioner with long travel in two dimensions (2023)

A precision positioning system is provided which provides long travel in two of the linear dimensions, while using non-contact bearings for both a first subassembly which provides long travel in one of the linear dimension and a second subassembly which provides long travel in the second linear dimension. The first or upper subassembly is preferably a magnetic subassembly which, in addition to providing long travel, also compensates or positions in three rotary dimensions and in the third linear dimension. The second subassembly is preferably either an air bearing or magnetic subassembly and is normally used only to provide long travel. Angled surfaces may be provided for magnetic bearings and capacitive or other gap sensing probes may be mounted to the stage and ground flush with the bearing actuators to provide more precise gap measurements.
Expression of Microcystis biosynthetic gene clusters in natural populations suggests temporally dynamic synthesis of novel and known secondary metabolites in western Lake Erie (2022)

Summary Microcystis spp. produces diverse secondary metabolites within freshwater cyanoHABs around the world. In addition to the biosynthetic gene clusters (BGCs) encoding known compounds, Microcystis genomes harbor numerous BGCs of unknown function, indicating its poorly understood chemical repertoire. While recent studies show that Microcystis produces several metabolites in the lab and field, little work has focused on analyzing the abundance and expression of its broader suite of BGCs during cyanoHAB events. Here, we use metagenomic and metatranscriptomic approaches to track the relative abundance of Microcystis BGCs and their transcripts throughout the 2014 western Lake Erie cyanoHAB. Results indicate the presence of several transcriptionally active BGCs that are predicted to synthesize both known and novel secondary metabolites. The abundance and expression of these BGCs shifted throughout the bloom, with transcript abundance levels correlating with temperature, nitrate and phosphorus concentrations, and the abundance of co-occurring predatory and competitive eukaryotic microorganisms, suggesting the importance of both abiotic and biotic controls in regulating expression. This work highlights the need for understanding the chemical ecology and potential risks to human and environmental health posed by secondary metabolites that are produced but unmonitored, as well as the potential discovery of pharmaceutical compounds from cyanoHAB-derived BGCs. Originality-Statement of Significance Microcystis spp . dominate cyanobacterial harmful algal blooms (cyanoHABs) worldwide and pose significant threats to water quality through the production of numerous secondary metabolites, many of which are toxic. While the toxicity and biochemistry of microcystins and several other compounds have been well studied, the broader suite of secondary metabolites produced by Microcystis remains poorly understood, leaving gaps in our understanding of their impacts on ecology, human and ecosystem health, or potential pharmaceutical application. In this study, we use metagenomic and transcriptomic datasets to examine the diversity of genes encoding synthesis of secondary metabolites in natural Microcystis populations and assess their patterns of transcription in the context of biotic and abiotic conditions in western Lake Erie cyanoHABs. Our results reveal the presence of a large diversity of both known gene clusters that encode toxic secondary metabolites as well as novel ones that encode cryptic compounds. This research highlights the need for targeted studies of the secondary metabolite diversity in western Lake Erie, a vital freshwater source to the United States and Canada.
Genetics and Early Detection in Idiopathic Pulmonary Fibrosis (2014)

Genetic studies hold promise in helping to identify patients with early idiopathic pulmonary fibrosis (IPF). Recent studies using chest computed tomograms (CTs) in smokers and in the general population have demonstrated that imaging abnormalities suggestive of an early stage of pulmonary fibrosis are not uncommon and are associated with respiratory symptoms, physical examination abnormalities, and physiologic decrements expected, but less severe than those noted in patients with IPF. Similarly, recent genetic studies have demonstrated strong and replicable associations between a common promoter polymorphism in the mucin 5B gene (MUC5B) and both IPF and the presence of abnormal imaging findings in the general population. Despite these findings, it is important to note that the definition of early-stage IPF remains unclear, limited data exist to definitively connect abnormal imaging findings to IPF, and genetic studies assessing early-stage pulmonary fibrosis remain in their infancy. In this perspective we provide updated information on interstitial lung abnormalities and their connection to IPF. We summarize information on the genetics of pulmonary fibrosis by focusing on the recent genetic findings of MUC5B. Finally, we discuss the implications of these findings and suggest a roadmap for the use of genetics in the detection of early IPF.
FDR Controlling Procedure for Multi-stage Analyses (2008)

Multiple testing has become an integral component in genomic analyses involving microarray experiments where large number of hypotheses are tested simultaneously. However before applying more computationally intensive methods, it is often desirable to complete an initial truncation of the variable set using a simpler and faster supervised method such as univariate regression. Once such a truncation is completed, multiple testing methods applied to any subsequent analysis no longer control the appropriate Type I error rates. Here we propose a modified marginal Benjamini \\&amp; Hochberg step-up FDR controlling procedure for multi-stage analyses (FDR-MSA), which correctly controls Type I error in terms of the entire variable set when only a subset of the initial set of variables is tested. The method is presented with respect to a variable importance application. As the initial subset size increases, we observe convergence to the standard Benjamini \\&amp; Hochberg step-up FDR controlling multiple testing procedure. We demonstrate the power and Type I error control through simulation and application to the Golub Leukemia data from 1999.
Analysis of the X-Ray Powder Diffraction Pattern of Neodymium Ammonium Hydroxynitrate: Nd(OH) 2 NO 3 .(NH 4 NO 3 ) 0.5 .H 2 O (1988)

Abstract Neodymium ammonium hydroxynitrate, Nd(OH) 2 NO 3 .(NH 4 NO 3 ) 0.5 .H 2 O, has been investigated by means of X-ray powder diffraction. Unit cell dimensions were determined by indexing programs, from diffractometer data obtained with strictly monochromatic CuK α 1 radiation. An I orthorhombic cell was found: a = 24.577 (4) Å, b = 7.1488 (16) Å, c = 3.8211 (9) Å. It is shown that the h 1 1 reflections present a selective line broadening.
Endocytotic uptake, processing, and retroendocytosis of human biosynthetic proinsulin by rat fibroblasts transfected with the human insulin receptor gene. (1988)

The cellular itinerary and processing of insulin and proinsulin were studied to elucidate possible mechanisms for the observed in vivo differences in the biologic half-lives of these two hormones. A rat fibroblast cell line transfected with a normal human insulin receptor gene was used. Due to gene amplification, the cells express large numbers of receptors and are ideal for studying a ligand, such as proinsulin, that has a low affinity for the insulin receptor. Competitive binding at 4 degrees C showed that the concentration of unlabeled insulin and proinsulin that is needed to displace 50% of tracer insulin or proinsulin was 0.85-0.95 nM and 140-150 nM, respectively. Binding to surface receptors and internalization occur at rates that are four to five times faster in cells incubated with insulin compared with proinsulin. Chloroquine led to an increase in cell-associated radioactivity of approximately 1.4-fold in cells incubated with insulin or proinsulin, but inhibited the appearance of degraded insulin by 54% and degraded proinsulin by only 10%. To study the fate of internalized ligand, cells were incubated with insulin and proinsulin until steady state binding occurred. Surface bound ligand was removed by an acid wash and the remaining cell-associated radioactivity represented internalized ligand. Cells were then reincubated in 37 degrees C buffer and the cell-associated radioactivity and radioactivity released into the medium were analyzed by TCA precipitation, Sephadex G-50, and HPLC. The results demonstrated that proinsulin more readily bypasses the intracellular degradative machinery and is therefore released intact from the cell via the retroendocytotic pathway. These results may help to explain the prolonged metabolic clearance rate and biologic responsiveness of proinsulin in vivo.
Kramers–Kronig detection of four 20  Gbaud 16-QAM channels using Kerr combs for a shared phase estimation (2020)

We experimentally demonstrate Kramers-Kronig detection of four 20 Gbaud 16-quadrature-amplitude-modulated (QAM) channels after 50 km fiber transmission using two soliton Kerr combs as signal sources and local oscillators. The estimated carrier phase at the receiver for each of the channels is relatively similar due to the coherence between the frequency comb lines. The standard deviation of the estimated carrier phase difference of the channels is less than 0.08 rad after 50 km single-mode fiber (SMF) transmission. This enables the carrier phase recovery derived from one channel to be shared among multiple channels. In the back-to-back scenario, the bit error rate (BER) performance for shared carrier phase recovery shows an optical signal-to-noise ratio penalty of ${\sim}{0.5}\;{\rm dB}$∼0.5dB compared to the BER performance for carrier phase recovery when derived for each channel independently. BERs below the forward error correction threshold are achieved after 50 km SMF transmission with both independent and shared carrier phase recovery for four 20-Gbaud 16-QAM signals.
Urine as a high-quality source of host genomic DNA from wild populations (2020)

Abstract The ability to generate genomic data from wild animal populations has the potential to give unprecedented insight into the population history and dynamics of species in their natural habitats. However, in the case of many species, it is impossible legally, ethically, or logistically to obtain tissues samples of high-quality necessary for genomic analyses. In this study we evaluate the success of multiple sources of genetic material (feces, urine, dentin, and dental calculus) and several capture methods (shotgun, whole-genome, exome) in generating genome-scale data in wild eastern chimpanzees ( Pan troglodytes schweinfurthii ) from Gombe National Park, Tanzania. We found that urine harbors significantly more host DNA than other sources, leading to broader and deeper coverage across the genome. Urine also exhibited a lower rate of allelic dropout. We found exome sequencing to be far more successful than both shotgun sequencing and whole-genome capture at generating usable data from low-quality samples such as feces and dental calculus. These results highlight urine as a promising and untapped source of DNA that can be noninvasively collected from wild populations of many species.
Experimental measurement of supercontinuum coherence in highly nonlinear soft-glass photonic crystal fibers (2017)

We present experimental measurements illustrating the power-dependent coherence evolution for supercontinuum generated in highly nonlinear SF6 photonic crystal fibers. The measurements were performed for fiber lengths close to and much longer than the soliton fission length. Simulations of the spectral evolution were also carried out to accompany the experimental observation. Many parameters were estimated by matching the simulated and the measured evolution. Both the measured and the simulated coherence evolution confirm the association between coherence degradation and soliton fission.
IBM POWER7 processor circuit design (2011)

The IBM POWER7® processor contains many innovative circuit ideas that enable advanced architectural features. A high-density embedded dynamic random access memory is used to provide 32 MB of level-3 cache. Improved input/output (I/O) links provide up to 50 GB/s of I/O bandwidth. An innovative phase-locked loop design allows for dynamic, per-core frequency variation, and unique multiport techniques for register files as well as six-transistor cell-based memory cells to support the superscalar multithreaded out-of-order processor.
Edge-AI: Rise of the neural accelerators (2019)

We are at the cusp of a new era in AI. Recently deep learning has revolutionised the field of Computer Vision, disrupting more traditional algorithmic approaches to object recognition, scene analysis and image understanding. But to date most of the applications of AI have relied on cloud-based services doing the heavy-lifting. Today we are at the cusp of a new era where AI data analysis is ready to move from the cloud and transition into the end device itself. In this talk we will review some of the Neural accelerators that are available today and look 1-2 years into the future to explore some of the potential impacts of edge-AI. We will also look at some of the new challenges and opportunities as AI migrates into individual devices: data-processing in the cloud won't go away, but more interestingly new computational &amp; storage demands will emerge to support training of edge-AI. Among these will be the rise of 'Fake Data' and the VR tools and associated infrastructure required to scale the training of advanced Edge-AI solutions.
Supplementary Data from Transcriptomic Correlates of Tumor Cell PD-L1 Expression and Response to Nivolumab Monotherapy in Metastatic Clear Cell Renal Cell Carcinoma (2023)

Supplementary Data from Transcriptomic Correlates of Tumor Cell PD-L1 Expression and Response to Nivolumab Monotherapy in Metastatic Clear Cell Renal Cell Carcinoma
An Overview of Classical and High Resolution Spectral Estimation (1980)

Current methods of spectral estimation can be broadly categorized under three main headings. One is classical power spectral density estimation which incorporates estimation of the autocorrelation function through lagged products and periodogram analysis and its variations. The second is power spectral density estimation based on modelling. This incorporates maximum entropy analysis, data extension using linear prediction and spectral estimation using ARMA models. The third is power spectral density estimation using adaptive windows which incorporates the method commonly referred to as the maximum likelihood (MLM) method. (Author)
On Over-Weighting the Bottom Line (2003)

Universities in the Marketplace The Commercialization of Higher Education. Derek Bok. Princeton University Press, Princeton, NJ, 2003. 247 pp. $22.95, £15.95. ISBN 0-691-11412-9. Bok discusses what he sees as the inherent dangers that arise when universities undertake money-making ventures with corporations.
Subjects with chronic lymphocytic leukaemia‐like B‐cell clones with stereotyped B‐cell receptors frequently show MDS‐associated phenotypes on myeloid cells (2014)

An increasing body of evidence suggests the potential occurrence of antigen encounter by the cell of origin in chronic lymphocytic leukaemia (CLL) and CLL-like monoclonal B-cell lymphocytosis (MBL). However, the scenario in which this event might occur remains unknown. In order to gain insight into this scenario we investigated the molecular, cytogenetic and haematological features of 223 CLL-like (n = 84) and CLL (n = 139) clones with stereotyped (n = 32) versus non-stereotyped (n = 191) immunoglobulin heavy chain variable region (IGHV) amino acid sequences. Overall, stereotyped CLL-like MBL and CLL clones showed a unique IGHV profile, associated with higher IGHV1 and lower IGHV3 gene family usage (P = 0·03), longer IGHV complementary determining region 3 (HCDR3) sequences (P = 0·007) and unmutated IGHV (P < 0·001) versus non-stereotyped clones. Whilst the overall size of the stereotyped B-cell clones in peripheral blood did not appear to be associated with the CLL-related cytogenetic profile of B-cells (P > 0·05), it did show a significant association with the presence of myelodysplastic syndrome (MDS)-associated immunophenotypes on peripheral blood neutrophils and/or monocytes (P = 0·01). Altogether our results point to the potential involvement of different selection forces in the expansion of stereotyped vs. non-stereotyped CLL and CLL-like MBL clones, the former being potentially favoured by an underlying altered haematopoiesis.
Impact of Evolutionary Changes in Nonalcoholic Fatty Liver Disease on Lung Function Decline (2022)

Regression of fatty liver is related to lung function decline. Continuing efforts to improve fatty liver may preserve lung function, especially for subjects with a high genetic risk.
Prefix and Address Assignment in a Home Network (2014)

This memo describes a home network prefix and address assignment
algorithm running on top of any 'flooding protocol' that
fulfills the specified requirements. It is expected that home border
routers are allocated one or multiple IPv6 prefixes through DHCPv6
Prefix Delegation (PD) or that prefixes are made available through
other means. An IPv4 address can also be assigned and private
addresses be used with NAT to provide IPv4 connectivity. In both
cases, provided prefixes need to be efficiently divided among the
multiple links, and routers need to obtain addresses. This document
describes a distributed algorithm for IPv4 and IPv6 prefixes division,
assignment and router's address assignment, and specifies how hosts
can be given addresses and configuration options using DHCP or SLAAC.
The Role of Nephrectomy and Metastasectomy for Advanced Renal Cell Carcinoma (2000)

Renal cell carcinoma (RCC) accounts for over 85% of all solid kidney tumors and is the third most common genitourinary malignancy after carcinoma of the prostate and bladder. Approximately 28–33,000 new cases of RCC are diagnosed per year in the United States, accounting for 3% of all adult malignancies, with an incidence roughly equal to that of all forms of leukemia combined (1). Over one third of patients with RCC will ultimately die of their disease. Despite the increase in incidentally discovered tumors due to the widespread use of noninvasive radiographic imaging techniques (2–4), 25–30% of patients present with locally advanced or metastatic disease (5). Delay in diagnosis may result from the ability of space occupying lesions of the retroperitoneum to become quite large before causing local symptoms. Additionally, manifestations of RCC are protean and may give rise to a constellation of nonspecific symptoms causing delayed detectionordiscovery ofthe lesionwhile pursuing otherdiagnoses. Finally, microscopic hematuria may go undetected while gross hematuria, which may occur only after the primary lesion has reached considerable size, may be improperly misattributed to other causes.
Thermal and Optical Characterization of Photonic Integrated Circuits by Thermoreflectance Microscopy (2009)

We report high resolution, non-invasive, thermal and optical characterization of semiconductor optical amplifiers (SOAs) and SOA-based photonic integrated circuits (PICs) using thermoreflectance microscopy. Chip-scale temperature imaging of SOAs and PICs, along with an energy balance model, are used to calculate the optical power distribution within and between SOAs to determine optical gain, fiber coupling loss, and passive component loss under normal device operating conditions. This technique is demonstrated to map optical power in SOA-based Mach-Zehnder interferometer (SOA-MZI) PICs, with close agreement with photocurrent and fiber-coupled measurements. The use of amplified spontaneous emission (ASE) for fiber-free characterization of the PICs is also shown, enabling non-invasive, wafer-scale testing prior to packaging.
A new design technique for optical links (2009)

A new optical link design technique is described. This technique provides an accurate measure of link performance. It can include a wide range of linear path degradations without requiring computer simulations of the link.
Acyclic analogs of nucleosides based on tris(hydroxymethyl)phosphine oxide: synthesis and incorporation into short DNA oligomers (2015)

Abstract Tris-(hydroxymethyl)phosphine oxide (THPO) to a certain extent resembles a part of 2′-deoxyribofuranose, although it exists in an acyclic form only and the oxygen atom at the THPO phosphorus center provides additional hydration site or acceptor of hydrogen bonds. After proper protection of hydroxyl groups, THPO was functionalized with nucleobases and converted into phosphoramidite monomers suitable for incorporation into growing oligonucleotide chains within the solid phase synthesis protocol. The resultant THPO-DNA analogs show reduced affinity to complementary DNA strands, and are resistant towards snake venom and calf spleen exonucleases.
ChemInform Abstract: SYNTHESIS OF (‐)‐SPATHULENOL (1981)

Abstract Ausgehend von (‐)‐Perillaaldehyd (erhältlich aus (‐)‐β‐Pinen) wird über die Stufen (II) (bekannte Überführung), (IV)‐(VIII) das Keton (IX) synthetisiert, dessen Umsetzung mit der Grignardverbindung (XI) ein Gemisch der Epimeren (XIIa) und (XIIb) liefert.
Further development of a reverse‐transcription loop‐mediated isothermal amplification (RT‐LAMP) assay for the detection of foot‐and‐mouth disease virus and validation in the field with use of an internal positive control (2020)

Foot-and-mouth disease (FMD) is a highly contagious viral disease of cloven-hooved animals. Global outbreaks have highlighted the significant economic, trade, psychosocial and animal welfare impacts that can arise from the detection of disease in previously 'FMD-free' countries. Rapid and early diagnosis provides significant advantages in disease control and minimization of deleterious consequences. We describe the process of further development and validation of a reverse-transcription loop-mediated isothermal amplification foot-and-mouth disease virus (RT-LAMP-FMDV) test, using a published LAMP primer set, for use in the field. An internal positive control (IPC) was designed and introduced for use with the assay to mitigate any intrinsic interference from the unextracted field samples and avoid false negatives. Further modifications were included to improve the speed and operability of the test, for use by non-laboratory trained staff operating under field conditions, with shelf-stable reaction kits which require a minimum of liquid handling skills. Comparison of the assay performance with an established laboratory-based real-time reverse transcriptase PCR (rRT-PCR) test targeting the 3D region of FMD virus (Tetracore Inc) was investigated. LAMP has the potential to complement current laboratory diagnostics, such as rRT-PCR, as a preliminary tool in the investigation of FMD. We describe a strategic approach to validation of the test for use in the field using extracted RNA samples of various serotypes from Thailand and then finally unextracted field samples collected from FMD-suspected animals (primarily oral lesion swabs) from Bhutan and Australia. The statistical approach to validation was performed by Frequentist and Bayesian latent class methods, which both confirmed this new RT-LAMP-FMDV test as fit-for-purpose as a herd diagnostic tool with diagnostic specificity >99% and sensitivity 79% (95% Bayesian credible interval: 65, 90%) on unextracted field samples (oral swabs).