gebhart/patrepeval huggingface dataset:
Allocating Bandwidth in Resilient Packet Ring Networks by Proportional Controller (2011)

The Resilient Packet Ring (RPR), defined under IEEE 802.17, has been proposed as a high-speed backbone technology for metropolitan area networks. RPR is introduced to mitigate the underutilization and unfairness problems associated with the current technologies such as SONET and Ethernet. The key performance objectives of RPR are to achieve high bandwidth utilization, optimum spatial reuse on the dual rings, and fairness. The challenge is to design an algorithm that can react dynamically to the traffics in achieving these objectives. The RPR fairness algorithm is comparatively simple, but it poses some critical limitations that require further investigation and remedy. One of the major problems is that the amount of bandwidth allocated by the algorithm oscillates severely under unbalanced traffic scenarios. These oscillations are barrier to achieving spatial reuse and high bandwidth utilization. Moreover, the performance of the RPR fairness algorithm is very sensitive to the algorithm parameters. In this paper, we apply Control Theory to solve the fairness issue, and construct a Proportional controller to dynamically adjust the fair rate in order to eliminate the state of congestion and to converge to the optimal fair rate.
Dissociating tinnitus patients from healthy controls using resting-state cyclicity analysis and clustering (2018)

Chronic tinnitus is a common and sometimes debilitating condition that lacks scientific consensus on physiological models of how the condition arises as well as any known cure. In this study, we applied a novel cyclicity analysis, which studies patterns of leader-follower relationships between two signals, to resting-state functional magnetic resonance imaging (rs-fMRI) data of brain regions acquired from subjects with and without tinnitus. Using the output from the cyclicity analysis, we were able to differentiate between these two groups with 58-67% accuracy by using a partial least squares discriminant analysis. Stability testing yielded a 70% classification accuracy for identifying individual subjects' data across sessions 1 week apart. Additional analysis revealed that the pairs of brain regions that contributed most to the dissociation between tinnitus and controls were those connected to the amygdala. In the controls, there were consistent temporal patterns across frontal, parietal, and limbic regions and amygdalar activity, whereas in tinnitus subjects, this pattern was much more variable. Our findings demonstrate a proof-of-principle for the use of cyclicity analysis of rs-fMRI data to better understand functional brain connectivity and to use it as a tool for the differentiation of patients and controls who may differ on specific traits.
Errors from Selective Disruption of the Editing Center in a tRNA Synthetase (2000)

Some aminoacyl-tRNA synthetases have two catalytic centers that together achieve fine-structure discrimination of closely similar amino acids. The role of tRNA is to stimulate translocation of a misactivated amino acid from the active site to the editing site where the misactivated substrate is eliminated by hydrolysis. Using isoleucyl-tRNA synthetase as an example, we placed mutations in the catalytic center for editing at residues strongly conserved from bacteria to humans. A particular single substitution and one double substitution resulted in production of mischarged tRNA, by interfering specifically with the chemical step of hydrolytic editing. The substitutions affected neither amino acid activation nor aminoacylation, with the cognate amino acid. Thus, because of the demonstrated functional independence of the two catalytic sites, errors of aminoacylation can be generated by selective mutations in the center for editing.
The purification and some properties of a stereospecific <scp>d</scp>-asparaginase from an extremely thermophilic bacterium, <i>Thermus aquaticus</i> (1982)

A specific D-asparaginase was isolated and crystallized from Thermus aquaticus strain T351. It is present in larger amounts than the L-asparaginase. The enzyme has a molecular weight of 60 000, an isoelectric point of 4.8 and a Km of 2 mM. It has 6 disulphide bonds/molecule, and a histidine residue at the active site. It is inhibited by keto acids and by high salt concentrations.
Rationale for Raising Current Clinical Practice Guideline Target for Serum 25-Hydroxyvitamin D in Chronic Kidney Disease (2019)

ERC therapy produced exposure-dependent reductions in plasma iPTH and bone turnover markers only when mean serum total 25-hydroxyvitamin D reached at least 50.8 ng/mL, indicating that current targets for vitamin D repletion therapy in CKD are too low. Gradual elevation of mean serum 25-hydroxyvitamin D to 92.5 ng/mL was not associated with significant adverse changes in safety parameters.
Chronic sodium nitrite therapy augments ischemia-induced angiogenesis and arteriogenesis (2008)

Chronic tissue ischemia due to defective vascular perfusion is a hallmark feature of peripheral artery disease for which minimal therapeutic options exist. We have reported that sodium nitrite therapy exerts cytoprotective effects against acute ischemia/reperfusion injury in both heart and liver, consistent with the model of bioactive NO formation from nitrite during ischemic stress. Here, we test the hypothesis that chronic sodium nitrite therapy can selectively augment angiogenic activity and tissue perfusion in the murine hind-limb ischemia model. Various therapeutic doses (8.25-3,300 mug/kg) of sodium nitrite or PBS were administered. Sodium nitrite significantly restored ischemic hind-limb blood flow in a time-dependent manner, with low-dose sodium nitrite being most effective. Nitrite therapy significantly increased ischemic limb vascular density and stimulated endothelial cell proliferation. Remarkably, the effects of sodium nitrite therapy were evident within 3 days of the ischemic insult demonstrating the potency and efficacy of chronic sodium nitrite therapy. Sodium nitrite therapy also increased ischemic tissue nitrite and NO metabolites compared to nonischemic limbs. Use of the NO scavenger carboxy PTIO completely abolished sodium nitrite-dependent ischemic tissue blood flow and angiogenic activity consistent with nitrite reduction to NO being the proangiogenic mechanism. These data demonstrate that chronic sodium nitrite therapy is a recently discovered therapeutic treatment for peripheral artery disease and critical limb ischemia.
Modeling and simulation of TDI CMOS image sensors (2013)

In this paper, a mathematical model of TDI CMOS image sensors was established in behavioral level through MATLAB based on the principle of a TDI CMOS image sensor using temporal oversampling rolling shutter in the along-track direction. The geometric perspective and light energy transmission relationships between the scene and the image on the sensor are included in the proposed model. A graphical user interface (GUI) of the model was also established. A high resolution satellitic picture was used to model the virtual scene being photographed. The effectiveness of the proposed model was verified by computer simulations based on the satellitic picture. In order to guide the design of TDI CMOS image sensors, the impacts of some parameters of TDI CMOS image sensors including pixel pitch, pixel photosensitive size, and integration time on the performance of the sensors were researched through the proposed model. The impacts of the above parameters on the sensors were quantified by sensor’s modulation transfer function (MTF) of the along-track direction, which was calculated by slanted-edge method. The simulation results indicated that the TDI CMOS image sensor can get a better performance with smaller pixel photosensitive size and shorter integration time. The proposed model is useful in the process of researching and developing a TDI CMOS image sensor.
Performance of a Distribution Intelligent Universal Transformer under Source and Load Disturbances (2006)

A bench model of the new generation intelligent universal transformer (IUT) has been recently developed for distribution applications. The distribution IUT employs high-voltage semiconductor device technologies along with multilevel converter circuits for medium-voltage grid connection. This paper briefly describes the basic operation of the IUT and its experimental setup. Performances under source and load disturbances are characterized with extensive tests using a voltage sag generator and various linear and nonlinear loads. Experimental results demonstrate that IUT input and output can avoid direct impact from its opposite side disturbances. The output voltage is well regulated when the voltage sag is applied to the input. The input voltage and current maintains clean sinusoidal and unity power factor when output is nonlinear load. Under load transients, the input and output voltages remain well regulated. These key features prove that the power quality performance of IUT is far superior to that of conventional copper-and-iron based transformers
Integrated biogas upgrading and hydrogen utilization in an anaerobic reactor containing enriched hydrogenotrophic methanogenic culture (2012)

Biogas produced by anaerobic digestion, is mainly used in a gas motor for heat and electricity production. However, after removal of CO(2) , biogas can be upgraded to natural gas quality, giving more utilization possibilities, such as utilization as autogas, or distant utilization by using the existing natural gas grid. The current study presents a new biological method for biogas upgrading in a separate biogas reactor, containing enriched hydrogenotrophic methanogens and fed with biogas and hydrogen. Both mesophilic- and thermophilic anaerobic cultures were enriched to convert CO(2) to CH(4) by addition of H(2) . Enrichment at thermophilic temperature (55°C) resulted in CO(2) and H(2) bioconversion rate of 320 mL CH(4) /(gVSS h), which was more than 60% higher than that under mesophilic temperature (37°C). Different dominant species were found at mesophilic- and thermophilic-enriched cultures, as revealed by PCR-DGGE. Nonetheless, they all belonged to the order Methanobacteriales, which can mediate hydrogenotrophic methanogenesis. Biogas upgrading was then tested in a thermophilic anaerobic reactor under various operation conditions. By continuous addition of hydrogen in the biogas reactor, high degree of biogas upgrading was achieved. The produced biogas had a CH(4) content, around 95% at steady-state, at gas (mixture of biogas and hydrogen) injection rate of 6 L/(L day). The increase of gas injection rate to 12 L/(L day) resulted in the decrease of CH(4) content to around 90%. Further study showed that by decreasing the gas-liquid mass transfer by increasing the stirring speed of the mixture the CH(4) content was increased to around 95%. Finally, the CH(4) content around 90% was achieved in this study with the gas injection rate as high as 24 L/(L day).
Apolipoprotein E Polymorphism and Alzheimer Disease (2000)

This first report of APOE*E4 and AD from the Indian subcontinent shows very low prevalence of AD in Ballabgarh, India, but association of APOE*E4 with AD at similar strength in Indian and US samples. Arch Neurol. 2000.
Dehydrogenation and cracking of C/sub 3/ and C/sub 4/ hydrocarbons to less saturated hydrocarbons (1986)

A method is described for converting feed hydrocarbons comprising at least one of C/sub 3/ and C/sub 4/ hydrocarbons to less saturated hydrocarbons, comprising: (a) establishing a body of cracking catalyst, in a reaction zone; (b) introducing the feed hydrocarbons into the upstream end of the body of catalyst; (c) passing the thus introduced feed hydrocarbons through the body of catalyst and in contact therewith; (d) withdrawing product hydrocarbons from the down-stream end of the body of catalyst; and (e) maintaining conditions within the body of catalyst sufficient to convert the feed hydrocarbons to the product hydrocarbons, including: a temperature in the upstream end of the body of catalyst between about 400/sup 0/C, and about 750/sup 0/C, and a temperature at the downstream end of the body of catalyst between about 100/sup 0/C, and about 200/sup 0/C, above the temperature in the upstream end.
Into Deep Water: Optimizing BCL6 Inhibitors by Growing into a Solvated Pocket (2021)

We describe the optimization of modestly active starting points to potent inhibitors of BCL6 by growing into a subpocket, which was occupied by a network of five stably bound water molecules. Identifying potent inhibitors required not only forming new interactions in the subpocket but also perturbing the water network in a productive, potency-increasing fashion while controlling the physicochemical properties. We achieved this goal in a sequential manner by systematically probing the pocket and the water network, ultimately achieving a 100-fold improvement of activity. The most potent compounds displaced three of the five initial water molecules and formed hydrogen bonds with the remaining two. Compound <b>25</b> showed a promising profile for a lead compound with submicromolar inhibition of BCL6 in cells and satisfactory pharmacokinetic (PK) properties. Our work highlights the importance of finding productive ways to perturb existing water networks when growing into solvent-filled protein pockets.
ChemInform Abstract: Recent Developments in the Chemistry, Biology and Medicine of the Epothilones (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 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.
Effect of AXIN2 expression on prostate cancer recurrence and an invasive, tumorigenic phenotype. (2015)

29 Background: Better biomarkers are needed in prostate cancer (PCa) to predict disease recurrence and guide optimal therapy. We investigated whether genes associated with a highly tumorigenic, drug resistant, progenitor cancer phenotype impact PCa biology and clinical outcomes in localized disease. Methods: Genes associated with self-renewal, drug resistance, and tumorigenicity were analyzed by qRT-PCR on PCa mRNA from radical prostatectomy (RP) specimens (+/- disease recurrence). Wilcoxon rank sum two-sample test, multivariable recursive partitioning, and bootstrap internal validation measured and confirmed associations with recurrence. Further validation was conducted in external cohorts and in-silico, as well as in vitro and in vivo using siRNA knockdown and lentiviral overexpression to determined the effect of gene expression on PCa proliferation, invasion and tumor growth. Results: Four candidate genes were differentially expressed in PCa recurrence, and of these, low AXIN2 expression was internally validated. Validation in external cohorts demonstrated low AXIN2 expression was associated with more aggressive prostate cancer and was independently associated with biochemical recurrence (BCR) and metastasis-free survival (MFS) after RP. In vitro, low AXIN2 expression was associated with a cancer stem-like cell-surface signature, and siRNA knockdown of AXIN2 resulted in significantly greater invasiveness. Conversely, ectopic overexpression of AXIN2 significantly reduced cell proliferation and tumor growth in mice. Conclusions: Low AXIN2 expression was associated with PCa recurrence after RP in our test population as well as in external validation cohorts. AXIN2 expression levels in PCa cells significantly impacted invasiveness, proliferation and tumor growth. AXIN2 represents a putative biomarker and potential therapeutic target in early prostate cancer.
Evaluation of a Minimally Invasive Cell Sampling Device Coupled with Assessment of Trefoil Factor 3 Expression for Diagnosing Barrett's Esophagus: A Multi-Center Case–Control Study (2015)

The Cytosponge-TFF3 test is safe and acceptable, and has accuracy comparable to other screening tests. This test may be a simple and inexpensive approach to identify patients with reflux symptoms who warrant endoscopy to diagnose BE.
SU‐GG‐T‐376: Medical Physics Calculations in the Cloud: A New Paradigm for Clinical Computing (2010)

Purpose: The accuracy of medical physics calculations is largely limited by the availability of fast computer hardware, which is in turn strongly limited by budget considerations. This research explores the use of the Cloud Computing paradigm to replace or supplement existing computing infrastructure for medical physics calculations. Cloud computing services allow for on‐demand virtual computing clusters with a pay‐as‐you‐go pricing model. This model has the potential to make large scale Monte Carlo simulations routine in clinical and research activities. Methods and materials: To test the feasibility of medical physics calculations in a cloud computing environment, a distributed Monte Carlo dose calculation framework was implemented with Amazon's EC2 cloud computing service, the Fluka 2008.3b Monte Carlo package, a distributed processing framework written in Python, and the Hadoop MapReduce framework. A variety of relevant calculations were performed: depth dose profiles of proton, electron, and photon beams, along with a simple proton treatment plan using a voxel patient geometry (Zubal phantom). The performance of EC2 was tested by running calculations on 1 to 200 virtual nodes with the different distributed processing frameworks. EC2 prices were compared with costs of comparable local hardware. Results: Relevant medical physics calculations were successfully carried out using the EC2 service. Heavy charged particle, electron, and photon depth dose profiles and a simple treatment plan were successfully calculated remotely. Performance data demonstrated the expected 1/n speed‐up as a function of node number. Two different distributed processing schemes were implemented in the cloud. Conclusion: Our implementations demonstrate the power of the existing cloud computing model. The relatively cheap pay‐as‐you‐go pricing for infrastructure on demand offers an extremely promising new paradigm for clinical and research computing, available to anyone with a network connection.
Ultrasound to video registration using a bi-plane transrectal probe with photoacoustic markers (2016)

Modern surgical scenarios typically provide surgeons with additional information through fusion of video and other imaging modalities. To provide this information, the tools and devices used in surgery must be registered together with interventional guidance equipment and surgical navigation systems. In this work, we focus explicitly on registering ultrasound with a stereo camera system using photoacoustic markers. Previous work has shown that photoacoustic markers can be used in this registration task to achieve target registration errors lower than the current available systems. Photoacoustic markers are defined as a set of non-collinear laser spots projected onto some surface. They can be simultaneously visualized by a stereo camera system and an ultrasound transducer because of the photoacoustic effect. In more recent work, the three-dimensional ultrasound volume was replaced by images from a single ultrasound image pose from a convex array transducer. The feasibility of this approach was demonstrated, but the accuracy was lacking due to the physical limitations of the convex array transducer. In this work, we propose the use of a bi-plane transrectal ultrasound transducer. The main advantage of using this type of transducer is that the ultrasound elements are no longer restricted to a single plane. While this development would be limited to prostate applications, liver and kidney applications are also feasible if a suitable transducer is built. This work is demonstrated in two experiments, one without photoacoustic sources and one with. The resulting target registration error for these experiments were 1.07mm±0.35mm and 1.27mm±0.47mm respectively, both of which are better than current available navigation systems.
A gate-coupled PTLSCR/NTLSCR ESD protection circuit for deep-submicron low-voltage CMOS ICs (1997)

A novel electrostatic discharge (ESD) protection circuit, which combines complementary low-voltage-triggered lateral SCR (LVTSCR) devices and the gate-coupling technique, is proposed to effectively protect the thinner gate oxide of deep submicron CMOS ICs without adding an extra ESD-implant mask. Gate-coupling technique is used to couple the ESD-transient voltage to the gates of the PMOS-triggered/NMOS-triggered lateral silicon controlled rectifier (SCR) (PTLSCR/NTLSCR) devices to turn on the lateral SCR devices during an ESD stress. The trigger voltage of gate-coupled lateral SCR devices can be significantly reduced by the coupling capacitor. Thus, the thinner gate oxide of the input buffers in deep-submicron low-voltage CMOS ICs can be fully protected against ESD damage. Experimental results have verified that this proposed ESD protection circuit with a trigger voltage about 7 V can provide 4.8 (3.3) times human-body-model (HBM) [machine-model (MM)] ESD failure levels while occupying 47% of layout area, as compared with a conventional CMOS ESD protection circuit.
Clinical Features Associated with Mutations in the Chromosome 1 Open-Angle Glaucoma Gene (<i>GLC1A</i>) (1998)

A variety of mutations in the GLC1A gene are associated with glaucoma. The spectrum of disease can range from juvenile glaucoma to typical late-onset primary open-angle glaucoma.
Validation of cAMP phosphodiesterase-4D7 (PDE4D7) for its independent contribution to risk stratification in a prostate cancer patient cohort with longitudinal biological outcomes. (2017)

5069 Background: In this study we present the retrospective validation of the prognostic prostate cancer biomarker PDE4D7 in predicting longitudinal biological outcomes in a historical cohort of radical prostatectomy patients. Methods: Biopsy punches from 550 patients were collected from a representative tumor area of FFPE surgical resections. RNA was extracted and PDE4D7 quantified by one-step RT-qPCR. PDE4D7 scores were calculated by normalization of PDE4D7 to the averaged expression of four reference genes. The independent prognostic value of the PDE4D7 scores were evaluated using uni- and multivariate Cox proportional hazard regression. Multivariate analyses were adjusted for clinical prognostic variables. Post-surgical outcomes tested were: PSA relapse, start of salvage treatment, progression to metastases, overall and prostate cancer specific mortality. Logistic regression was used to create a combined prognostic model of PDE4D7 with clinical risk and tested in outcome prediction. Results: The PDE4D7 score was significantly associated with time to PSA failure after prostatectomy (HR 0.53; 95% CI 0.41-0.67 for each unit increase; p < 1.0E-04). After adjustment for pathology Gleason, pT stage, surgical margin status, and seminal vesicle invasion the HR was 0.55 (95% CI 0.43-0.72; p < 1.0E-04). Patients with a high PDE4D7 score that were clinically classified as intermediate to high risk of progression were re-classified into a group with an average progression risk less than the average cohort risk of clinically very low risk patients. The maximum benefit, compared to Gleason score, was observed in the clinically intermediate favorable risk group. Combining clinical risk with PDE4D7 scores improved the overall risk stratification. Conclusions: The PDE4D7 score has potential to provide independent risk information and, in particular, to re-stratify patients with clinical intermediate to high risk characteristics to a very low risk profile.
Paper Microfluidics Goes Digital (2014)

The first example of so-called "digital microfluidics" (DMF) implemented on paper by inkjet printing is reported. A sandwich enzyme-linked immunosorbent assay (ELISA) is demonstrated as an example of a complex, multistep protocol that would be difficult to achieve with capillary-driven paper microfluidics. Furthermore, it is shown that paper-based DMF devices have comparable performance to traditional photolithographically patterned DMF devices at a fraction of the cost.