gebhart/patrepeval huggingface dataset:
Culture independent analysis of ileal mucosa reveals a selective increase in invasive <i>Escherichia coli</i> of novel phylogeny relative to depletion of Clostridiales in Crohn's disease involving the ileum (2007)

Intestinal bacteria are implicated increasingly as a pivotal factor in the development of Crohn's disease, but the specific components of the complex polymicrobial enteric environment driving the inflammatory response are unresolved. This study addresses the role of the ileal mucosa-associated microflora in Crohn's disease. A combination of culture-independent analysis of bacterial diversity (16S rDNA library analysis, quantitative PCR and fluorescence in situ hybridization) and molecular characterization of cultured bacteria was used to examine the ileal mucosa-associated flora of patients with Crohn's disease involving the ileum (13), Crohn's disease restricted to the colon (CCD) (8) and healthy individuals (7). Analysis of 16S rDNA libraries constructed from ileal mucosa yielded nine clades that segregated according to their origin (P<0.0001). 16S rDNA libraries of ileitis mucosa were enriched in sequences for Escherichia coli (P<0.001), but relatively depleted in a subset of Clostridiales (P<0.05). PCR of mucosal DNA was negative for Mycobacterium avium subspecies paratuberculosis, Shigella and Listeria. The number of E. coli in situ correlated with the severity of ileal disease (rho 0.621, P<0.001) and invasive E. coli was restricted to inflamed mucosa. E. coli strains isolated from the ileum were predominantly novel in phylogeny, displayed pathogen-like behavior in vitro and harbored chromosomal and episomal elements similar to those described in extraintestinal pathogenic E. coli and pathogenic Enterobacteriaceae. These data establish that dysbiosis of the ileal mucosa-associated flora correlates with an ileal Crohn's disease (ICD) phenotype, and raise the possibility that a selective increase in a novel group of invasive E. coli is involved in the etiopathogenesis to Crohn's disease involving the ileum.
The membrane‐bound [NiFe]‐hydrogenase (Ech) from <i>Methanosarcina barkeri</i>: unusual properties of the iron‐sulphur clusters (2002)

The purified membrane-bound [NiFe]-hydrogenase from Methanosarcina barkeri was studied with electron paramagnetic resonance (EPR) focusing on the properties of the iron-sulphur clusters. The EPR spectra showed signals from three different [4Fe-4S] clusters. Two of the clusters could be reduced under 101 kPa of H2, whereas the third cluster was only partially reduced. Magnetic interaction of one of the clusters with an unpaired electron localized on the Ni-Fe site indicated that this was the proximal cluster as found in all [NiFe]-hydrogenases. Hence, this cluster was assigned to be located in the EchC subunit. The other two clusters could therefore be assigned to be bound to the EchF subunit, which has two conserved four-Cys motifs for the binding of a [4Fe-4S] cluster. Redox titrations at different pH values demonstrated that the proximal cluster and one of the clusters in the EchF subunit had a pH-dependent midpoint potential. The possible relevance of these properties for the function of this proton-pumping [NiFe]-hydrogenase is discussed.
AtomRace (2008)

The paper proposes a novel algorithm called AtomRace for a dynamic detection of data races. Data races are detected as a special case of atomicity violations on atomic sections specially defined to span just particular read/write instructions and the transfer of control to and from them. A key ingredient allowing AtomRace to efficiently detect races on such short atomic sections is a use of techniques for a careful injection of noise into the scheduling of the monitored programs. The approach is very simple, fully automated, avoids false alarms, and allows for a lower overhead and better scalability than many other existing dynamic data race detection algorithms. We illustrate these facts by a set of experiments with a prototype implementation of AtomRace. Further, AtomRace can also be applied to detect atomicity violations on more general atomic sections than those used for the data race detection. They can be defined by the user or obtained by some static analysis.
A Hybrid-Mode Operational Transconductance Amplifier for an Adaptively Biased Low Dropout Regulator (2016)

This paper presents a hybrid-mode, operational transconductance amplifier (HM-OTA) to improve the dynamic response of an adaptively biased low dropout regulator (AB-LDR) while maintaining a low quiescent current. Using the proposed HMOTA in the AB-LDR, we can achieve higher dc gain and wider loop bandwidth compared to a conventional current-mode OTA (CM-OTA). Additionally, the proposed HM-OTA provides a high discharging slew-rate at the gate of the PMOS power transistor during a low-to-high load step. So, the proposed HM-OTA helps to achieve a good dc load regulation as well as a reduced undershoot during load transient. At the same time, the regulator requires a small value of the output capacitor for achieving the loop stability compared to the conventional differential-mode OTA (DM-OTA). The conventional CM-OTA and the DM-OTA turn out to be special cases of the proposed HM-OTA that does not occupy extra space in silicon or consume additional power to realize. The AB-LDR using the proposed HM-OTA has been implemented in 0.18-μm CMOS technology. The regulator consumes a quiescent current of 1.6-μA at the no-load condition with a transient variation of 24 mV at V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">o</sub> = 1.2 V for 0-50 mA of load step with a 1-μF output capacitor.
Labeled PSI from Fully Homomorphic Encryption with Malicious Security (2018)

Private Set Intersection (PSI) allows two parties, the sender and the receiver, to compute the intersection of their private sets without revealing extra information to each other. We are interested in the unbalanced PSI setting, where (1) the receiver's set is significantly smaller than the sender's, and (2) the receiver (with the smaller set) has a low-power device. Also, in a Labeled PSI setting, the sender holds a label per each item in its set, and the receiver obtains the labels from the items in the intersection. We build upon the unbalanced PSI protocol of Chen, Laine, and Rindal (CCS~2017) in several ways: we add efficient support for arbitrary length items, we construct and implement an unbalanced Labeled PSI protocol with small communication complexity, and also strengthen the security model using Oblivious Pseudo-Random Function (OPRF) in a pre-processing phase. Our protocols outperform previous ones: for an intersection of 220 and $512$ size sets of arbitrary length items our protocol has a total online running time of just $1$~second (single thread), and a total communication cost of 4 MB. For a larger example, an intersection of 228 and 1024 size sets of arbitrary length items has an online running time of $12$ seconds (multi-threaded), with less than 18 MB of total communication.
Full Surface Embedding of Gold Clusters on Silicon Nanowires for Efficient Capture and Photothermal Therapy of Circulating Tumor Cells (2012)

We report on rapid thermal chemical vapor deposition growth of silicon nanowires (Si NWs) that contain a high density of gold nanoclusters (Au NCs) with a uniform coverage over the entire length of the nanowire sidewalls. The Au NC-coated Si NWs with an antibody-coated surface obtain the unique capability to capture breast cancer cells at twice the highest efficiency currently achievable (~88% at 40 min cell incubation time) from a nanostructured substrate. We also found that irradiation of breast cancer cells captured on Au NC-coated Si NWs with a near-infrared light resulted in a high mortality rate of these cancer cells, raising a fine prospect for simultaneous capture and plasmonic photothermal therapy for circulating tumor cells.
Removal of redundancy in logic circuits under classification of undetectable faults (2003)

The authors describe a method for removing redundant elements using test pattern generation. Redundancy in combinational circuits can be identified from the existence of undetectable stuck-at faults. By classifying undetectable faults into three categories according to their properties obtained in the test pattern generation process, some redundant elements can be concurrently removed. The method produces an irredundant circuit efficiently by using these properties. An improved procedure for redundancy removal is outlined to reduce the number of repetitions of test generation performed in the process. Some environmental results for ISCAS 85 benchmark circuits are also shown.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Two distinct mechanisms for stimulation of oxygen-radical production by polymorphonuclear leucocytes (1983)

Oxygen-radical production stimulated from rat polymorphonuclear leucocytes by either unopsonized latex particles (diameter = 1.01 microM) or chemotactic peptide (N-formyl-Met-Leu-Phe) was monitored by using luminol-dependent chemiluminescence. Azide inhibited by more than 80% the luminescence response induced by chemotactic peptide whether added before or after stimulation. However, the luminescence response to latex particles was progressively less susceptible to azide inhibition if the azide was added after the stimulus. Cytochalasin B, which was shown to abolish phagocytosis of the latex beads, also abolished the chemiluminescence response. However, the same cells showed a greatly enhanced response to chemotactic peptide. Cytochalasin B-treated cells secreted approx. 45% of total cellular myeloperoxidase in response to chemotactic peptide, but there was no detectable secretion in response to unopsonized latex particles. Microperoxidase equivalent to 20% of cellular peroxidase activity added to the cells before addition of the stimulus had no effect on the response to latex particles but increased approx. 2-fold the peak rate of chemiluminescence induced by chemotactic peptide. It was concluded that the unopsonized latex particles stimulated oxygen-radical production by the mechanism that involved endocytosis, whereas chemotactic peptide stimulated production by a mechanism that involved exocytosis of myeloperoxidase, the latter mechanism requiring an increase in intracellular free [Ca2+].
Human genomes as email attachments (2008)

The amount of genomic sequence data being generated and made available through public databases continues to increase at an ever-expanding rate. Downloading, copying, sharing and manipulating these large datasets are becoming difficult and time consuming for researchers. We need to consider using advanced compression techniques as part of a standard data format for genomic data. The inherent structure of genome data allows for more efficient lossless compression than can be obtained through the use of generic compression programs. We apply a series of techniques to James Watson's genome that in combination reduce it to a mere 4MB, small enough to be sent as an email attachment.
Near-optimal precharging in high-performance nanoscale CMOS caches (2003)

High-performance caches statically pull up the bit-lines in all cache subarrays to optimize cache access latency. Unfortunately, such architecture results in a significant waste of energy in nanoscale CMOS implementations due to high leakage and bitline discharge in the unaccessed subarrays. Recent research advocates bitline isolation to control precharging of individual subarrays using bitline precharge devices. In this paper, we carefully evaluate the energy and performance trade-offs of bitline isolation, and propose a technique to exploit nearly its full potential to eliminate discharge and reduce overall energy in level-one caches. Cycle-accurate and circuit simulation results of a wide-issue superscalar processor indicate that: 1) in future CMOS technologies (e.g., 70 nm and beyond), cache architectures that exploit bitline isolation can eliminate up to 90% of the bitline discharge; 2) on-demand precharging (i.e., decoding the address and subsequently precharging the accessed subarrays) is not viable in level-one caches because precharging increases the cache access latency; and 3) our proposal for gated precharging to exploit subarray reference locality and precharging only the recently accessed subarrays eliminates nearly all of bitline discharge in nanoscale CMOS caches with only a 1% of performance degradation.
Seroflocculating Steroids. VIII.<sup>1</sup> Side Chain Reduction of Deoxycholic, 12α-Hydroxy-3-cholenic and 3α-Hydroxy-11-cholenic Acids<sup>2</sup> (1959)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSeroflocculating Steroids. VIII.1 Side Chain Reduction of Deoxycholic, 12α-Hydroxy-3-cholenic and 3α-Hydroxy-11-cholenic Acids2Robert T. Blickenstaff and Frederic C. ChangCite this: J. Am. Chem. Soc. 1959, 81, 11, 2835–2838Publication Date (Print):June 1, 1959Publication History Published online1 May 2002Published inissue 1 June 1959https://pubs.acs.org/doi/10.1021/ja01520a056https://doi.org/10.1021/ja01520a056research-articleACS PublicationsRequest reuse permissionsArticle Views62Altmetric-Citations9LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Fluid Durability in a High Speed Electro-Rheological Clutch (1993)

The durability of an electro-rheological (ER) fluid was investigated by running a high speed ER clutch under different conditions and periods of operation. The tests involved running the clutch at 3000 rpm for a total period of twelve hours over a five day period. The tests subjected the fluid to a centripetal acceleration of 3000 m/s 2 , and were conducted with and without an excitation field of 2 kV/mm, and with and without shearing the fluid at shear rates up to 9500 s -1 . The condition of the fluid was assessed periodically by measuring the torque response of the clutch to a step ap plication of voltage in respect of both magnitude and speed of response. Results at the two pole 50 Hz synchronous speed of 3000 rpm indicated that the particles in the fluid were centrifuged over the prolonged test periods. The application of a voltage across the fluid had a negligible effect on this particle migration. The effect of particle migration due to centrifugal and electro-static effects indicate future development requirements for these smart materials.
Magnesium Lithospermate B Suppresses the Increase of Active Oxygen in Rats after Subtotal Nephrectomy (1997)

Subtotally nephrectomized rats were found to have decreased activities of superoxide dismutase (SOD) and catalase, and spin trapping with 5,5-dimethyl-1-pyrroline-N-oxide (DMPO) showed that the amount of hydroxyl radical in the residual kidney tissue was greater than that in normal rat kidney. This indicated both direct and indirect involvement of free radicals in renal failure. In contrast, rats given magnesium lithospermate B (10 mg/kg body weight) orally for 30 days after subtotal nephrectomy showed restoration of SOD and catalase activities to almost normal levels. Hydroxyl radical, which is highly reactive and for which there is no scavenger system in the body, was decreased markedly in kidney homogenates obtained from rats given magnesium lithospermate B and in an experimental system for hydroxyl radical production to which magnesium lithospermate B was directly added. The increased levels of uremic toxins in the blood were also low in rats given magnesium lithospermate B. This indicates that magnesium lithospermate B helps to inhibit the progression of renal failure by scavenging radicals.
Estimate round trip time of TCP in a passive way (2005)

With the development of Internet, service performance measurement, becomes a technical hotspot. In this paper, a passive RTT estimate algorithm (PRE) is proposed to estimate round trip time (RlT) of long-term TCP in the broadband network. Since TCP sender always sends packages that belong to the same round together, there is a "gap" between two rounds of sending. PRE can find "gap" between two rounds, and so (hat can estimate RTf in a passive mode. Base on PRE, passive TCP performance measurement can be deployed in the traffic monitors. Both simulation and practical experiments validate that the algorithm can estimate RTT properly.
Zinc finger protein (ZFP) in plants-a review (2013)

Zinc finger protein (ZFP) possesses one or more 'zinc finger' that bond one or more zinc ions by its residues Histidine (His) and Cysteine (Cys). ZFP also belongs to a large family of transcription factor. It plays many important regulatory roles in plants. Here, we explained that the percentage of ZFP transcription factor in total transcription factors is similar among plant species. The ZFP functions were implicated in development, growth, stress response and phytohormone responses based on the conclusion of four ZFP families, C2H2, CCCH, C3HC4 and C4. Meanwhile, there was one main function in each ZFP family. On the basis of analyses of the ZFP gene expression in the CCCH family of rice, the regulation controlled by rice ZFP in various tissues was significantly related with each other, as well as in responses to different abiotic stresses. Expression of some rice tissues-specific ZFP genes was significantly related to abiotic or biotic stresses.
Quantitative analysis of erythrocytes containing fetal hemoglobin (F cells) in children with sickle cell disease (1997)

Variation in the level of fetal hemoglobin (HbF) accounts for much of the clinical heterogeneity observed in patients with sickle cell disease (SCD). The HbF level has emerged as an important prognostic factor in both sickle cell pain and mortality, and a % HbF of 10-20% has been suggested as a threshold level for diminished clinical severity. The number of erythrocytes that contain HbF (termed F cells) may also be critically important, as F cells resist intravascular sickling and have preferential in vivo survival. Since F cells can be enumerated with high accuracy using flow cytometry methods, we prospectively studied a cohort of 242 children with SCD. Children with HbS and hereditary persistence of fetal hemoglobin (S/HPFH) had essentially 100% F cells. In contrast, children with homozygous sickle cell anemia (HbSS), HbS/beta0 thalassemia, or HbS/beta+ thalassemia had significantly lower mean % F cell values (55.9, 61.6, and 51.3%, respectively; P < 0.001), and children with HbSC had even fewer F cells (27.0%; P < 0.001). There was a highly significant correlation between the % F cells and the log (% HbF), which was observed for the total population of children (r = 0.95, P < 0.001), as well as for each of the individual subgroups of children with HbSS (r = 0.94, P < 0.001), HbSC (r = 0.89, P < 0.001), or HbS/beta0 thalassemia and HbS/beta+ thalassemia (r = 0.95, P <0.001). This logarithmic correlation between % F cells and % HbF has not been previously described and has important implications for the pharmacologic manipulation of HbF in patients with SCD.
Generation of carrier-suppressed broad pulses from modelocked DBR laser operating with two carrier wavelengths (2006)

A method is presented to generate a carrier-suppressed (CS) optical pulse train from a modelocked distributed Bragg reflector laser diode operating with two carrier wavelengths. Generation of 40 GHz CS broad pulse trains at 40 GHz was successfully achieved with tunable pulse width from 10.3 to 15.9 ps.
SIMILARITY EVALUATION OF ONLINE SIGNATURES BASED ON MODIFIED DYNAMIC TIME WARPING (2013)

Many people are very accustomed to the process of signing their name and having it matched for authentication. In a signature verification system, the signatures are processed to extract features that are used for verification. These features should not be duplicable. A basic problem is intraclass variations that will greatly affect the matching scores produced. The problem of distinctiveness occurs when the expectation of signatures to vary significantly between individuals is not met. There may be a large number of similarities in the feature sets used to represent the signatures of two different individuals. The efficiency of any signature verification system depends mainly on the discrimination power and robustness of the features used in the system. This study evaluates 40 functional features of viewpoint classification error and consistency for extracting the best subset once a set of features provides maximal discrimination capability between genuine and forged signatures. A modified distance of the DTW algorithm is proposed to improve performance of the verification phase. The proposed system is evaluated on the public SVC2004 signature database. The experimental results show that first, the most discriminate and consistent features are velocity based. Second, the average EER for the proposed algorithm in comparison with the general DTW algorithm shows a 5.47% decrease. Moreover, a comparative study based on a different classifier with a skilled forgery shows that the best result has an EER of 1.73% using the Parzen window classifier.
Potassium–Argon Age Studies in Scotland (1965)

Abstract New potassium-argon age determinations are presented for rocks ranging in age from Lewisian to Tertiary. A late-Caledonian metamorphic event at about 422 million years is very important in the Highlands and the relationship of this to previous metamorphisms is discussed. Newer Granite emplacement took place about 400 million years ago and the Moine thrust movement also took place at about this date. Lower Carboniferous basalts yield, by whole rock methods, ages compatible with the time scales of Kulp (1960) and Holmes (1959). Volcanic activity in Mull is confirmed as Palaeocene or Eocene in age.