gebhart/patrepeval huggingface dataset:
Clinical Utility of Circulating Tumor Cell Measurement in the Diagnosis of Indeterminate Lesions of the Pancreas (2009)

The quantification of circulating tumor cells has been historically problematic due to the different methods applied to their measurement. Following the development of standardized technology, they are now becoming well-established prognostic and predictive markers in patients with breast, colon and prostate cancer. While they represent a real-time noninvasive test, their use in diagnostics has seldom been reported. We report their use to help diagnose an indeterminate pancreatic mass. The use of an automated circulating tumor cell platform as described is likely to have utility as an aid to differential diagnosis, although larger studies will be required to ascertain its positive or negative predictive value.
Field-varying aberration recovery in EUV microscopy using mask roughness (2018)

We derive and solve a simplified, self-calibrated inverse problem to characterize the field-dependent aberrations of an EUV synchrotron-based full-field microscope, using images of the surface roughness of an EUV photomask under several angles of illumination. We demonstrate diffraction-limited imaging performance at the center of its field-of-view.
ChemInform Abstract: Borate Esters. Part 7. Borate Esters of Some 1,3‐Diones. (1988)

Abstract According to an NMR study, the formation of borate diesters (IV) is preferred to that of borate monoesters (III).
Long-Term Safety and Efficacy of Certolizumab Pegol Therapy in Patients With Moderate to Severe Crohnʼs Disease: 5-Year Results (2015)

Introduction: Certolizumab pegol (CZP) is approved in the US for the treatment of moderate to severe Crohn's disease (CD). The aim of this open-label extension, C87088, was to assess the long-term safety and efficacy of CZP in patients (pts) with CD who had previously participated in C87085, a 6-week, randomized, double-blind, placebo-controlled study of CZP, evaluating induction of remission. Methods: Pts who became worse in the first two weeks of the C87085 protocol (Crohn's disease activity index [CDAI] ≥70 points relative to baseline or an absolute CDAI ≥350 points) and those who completed Week 6 of C87085 were eligible for inclusion in C87088. All pts received an induction regimen of CZP 400 mg at Weeks 0, 2, and 4, then maintenance therapy of CZP 400 mg every 4 weeks until Week 262. The proportion of pts in clinical remission (Harvey-Bradshaw Index [HBI] score of ≤4 points/Inflammatory Bowel Disease Questionnaire [IBDQ] score of ≥170 points) over 5 years were calculated using an observed case (OC) analysis (where pts who withdrew were excluded from the denominator) or a non-remitter imputation (NRI) analysis (where pts who withdrew or whose efficacy-related adverse events [AEs] led to withdrawal [including exacerbation of CD] were included in the denominator). AEs were summarized descriptively and incidence rates (IR) and 95% confidence intervals (95% CI) per 100 pt-years were calculated. Results: Pts (n=402) had a mean age of 37.3 years and a mean duration of CD of 7.2 years. The OC remission rates over time using HBI ranged from 65.2% at Week 52 to 85.2% at Week 262; and from 38.9% to 14.9% for NRI (Figure 1a). Using IBDQ, OC remission rates ranged from 63.9% at Week 52 to 67.4% at Week 262; and from 37.8% to 10.0% for NRI (Figure 1b). AEs were reported by 89.6% of pts and serious AEs by 37.1%. The IR (95% CI) of infections was 4.09 (2.85, 5.69)/100 pt-years, with 1 case of pulmonary tuberculosis being reported in a Romanian pt. The IR of neoplasms (benign, malignant, unspecified) was 1.00 (0.46, 1.90)/100 pt-years, with 4 cases of basal cell carcinoma being reported. One pt died of pulmonary thromboarteritis.Figure 1Conclusion: In this open-label extension study, a sizeable proportion of patients treated with CZP achieved and maintained clinical remission up to 5 years. No new safety signals were detected with longterm CZP exposure. Clinicaltrials.gov identifier: NCT00552344. Statement of funding: This study was sponsored by UCB Pharma.
Anti-HIV host factor SAMHD1 regulates viral sensitivity to nucleoside reverse transcriptase inhibitors via modulation of cellular deoxyribonucleoside triphosphate (dNTP) levels. (2014)

VOLUME 288 (2013) PAGES 20683–20691 National Institutes of Health Grant AI077401 (to B. K.) was cited incorrectly. The correct grant number is National Institutes of Health Grant GM104198 (to B. K.).
FIGURE 2 from A Novel Class of Ribosome Modulating Agents Exploits Cancer Ribosome Heterogeneity to Selectively Target the CMS2 Subtype of Colorectal Cancer (2023)

&lt;p&gt;ZKN-157 selectively inhibits new protein synthesis in a sensitive colorectal cancer cell line. &lt;b&gt;A,&lt;/b&gt; Volcano plot showing heavy-isotope intensities (newly synthesized protein abundance) for 2867 proteins detected at 24-hour timepoint. Protein were classified as follows: Decreased (log&lt;sub&gt;2&lt;/sub&gt;FC &lt; −0.4, &lt;i&gt;P&lt;/i&gt;&lt;sub&gt;adjusted&lt;/sub&gt; &lt; 0.05, red), Downward Trend (log&lt;sub&gt;2&lt;/sub&gt;FC &lt; −0.4, &lt;i&gt;P&lt;/i&gt;&lt;sub&gt;adjusted&lt;/sub&gt; &gt; 0.05, pink), Increased (log&lt;sub&gt;2&lt;/sub&gt;FC &gt; 0.4, &lt;i&gt;P&lt;/i&gt;&lt;sub&gt;adjusted&lt;/sub&gt; &lt; 0.05, dark green), Upward Trend (log&lt;sub&gt;2&lt;/sub&gt;FC &gt; 0.4, &lt;i&gt;P&lt;/i&gt;&lt;sub&gt;adjusted&lt;/sub&gt; &gt; 0.05, light green), Unchanged (−0.4 &lt; log&lt;sub&gt;2&lt;/sub&gt;FC &lt; 0.4, &lt;i&gt;P&lt;/i&gt;&lt;sub&gt;adjusted&lt;/sub&gt; &gt; 0.05, dark gray). Dotted lines indicate −0.5 and 0.5 log&lt;sub&gt;2&lt;/sub&gt;FC values. &lt;b&gt;B,&lt;/b&gt; Bar graph plotting percent protein fraction of heavy-isotope intensity (categorized as in &lt;b&gt;A&lt;/b&gt;) at 24-hour timepoint versus positively charged regions. Positive charge windows were generated by assigning K and R residues a positive 1 charge and all other amino acid residues a charge of 0. Average charge values were then calculated along a 10-amino acid long sliding window for each protein's amino acid sequence (starting at the first residue and ending at the last complete set of 10 residues). &lt;b&gt;C,&lt;/b&gt; Overrepresentation analysis and pathway enrichment in significantly downregulated proteins from &lt;b&gt;A&lt;/b&gt; are shown. Count refers to the number of genes found in each pathway while gene ratio refers to the count divided by all genes in the pathway. &lt;b&gt;D,&lt;/b&gt; Bar graph showing nascent protein abundance for 68 Ribosomal proteins from heavy-isotope intensity analysis at 24-hour timepoint (categorized as in &lt;b&gt;A&lt;/b&gt;). The dotted line indicates −0.4 log&lt;sub&gt;2&lt;/sub&gt;FC value.&lt;/p&gt;
MR-FoodCoach: Enabling a convenience store on mixed reality space for healthier purchases (2022)

We study ways to improve the shopping experience in a mixed-reality environment. In the demonstration, the participants would experience the concept of mixed-reality-enabled convenience stores for healthier purchases. Over Microsoft HoloLens2, anywhere can become a convenience store where physical and virtual foods can be recognized and deployed. The prototype would help customers with healthier purchases. For each product, its nutrition facts and even an intuitive metric, NutriScore, are available for customers. Furthermore, the visualization of its footsteps in supply chains over the globe would guarantee transparency of its origin. GS1 EPCIS standard and temporal reachability computation enable the demonstration.
Algorithm selection: a quantitative optimization-intensive approach (1999)

Implementation platform selection is an important component of hardware-software codesign process which selects, for a given computation, the most suitable implementation platform. In this paper, we study the complementary component of hardware-software codesign, algorithm selection. Given a set of specifications for the targeted application, algorithm selection refers to choosing the most suitable completely specified computational structure for a given set of design goals and constraints, among several functionally equivalent alternatives. While implementation platform selection has been recently widely and vigorously studied, the algorithm selection problem has not been studied in computer-aided design domain until now. We first introduce the algorithm selection problem, and then analyze and classify its degrees of freedom. Next, we demonstrate an extraordinary impact of algorithm selection for achieving high throughput, and low-cost implementations. We define the algorithm selection problem formally and prove that throughput and area optimization using algorithm selection are computationally intractable problems. We also propose a relaxation-based heuristic for throughput optimization. Finally, we present an algorithm for cost optimization using algorithm selection. The effectiveness of methodology and proposed algorithms is illustrated using real-life examples.
Correlation analysis on large-scale wind power—with Qian’An base’s field data (2015)

Renewable energy has become an important solution to the sustainable development strategy of energy in the world, which is facing the problem of fossil fuel depletion, environmental pollution, and climate change. Among them, wind power has been developed a lot, with the advantages of rich reserves, lower costs, environmentally friendly generating process, and mature technology [1].
AN EFFECT OF ANTIGEN-ANTIBODY INTERACTION ON BLOOD COAGULATION (1959)

Each of several antigen-antibody systems studied has been found to affect the coagulation mechanism in the rabbit, causing a marked shortening of the coagulation time in vitro of samples of whole blood maintained in siliconized glassware. Addition of specific antigen to the blood of actively immunized animals or addition of antigen-antibody mixtures to the blood of normal animals produced the effect. The coagulation time of plasma was not affected, indicating that the phenomenon may be mediated by an effect on platelets. This effect of antigen-antibody interaction may be involved in the production of tissue damage in vivo.
Dark energy, inflation, and extra dimensions (2009)

We consider how accelerated expansion, whether due to inflation or dark energy, imposes strong constraints on fundamental theories obtained by compactification from higher dimensions. For theories that obey the null energy condition (NEC), we find that inflationary cosmology is impossible for a wide range of compactifications; and a dark energy phase consistent with observations is only possible if both Newton's gravitational constant and the dark energy equation of state vary with time. If the theory violates the NEC, inflation and dark energy are only possible if the NEC-violating elements are inhomogeneously distributed in the compact dimensions and vary with time in precise synchrony with the matter and energy density in the noncompact dimensions. Although our proofs are derived assuming general relativity applies in both four and higher dimensions and certain forms of metrics, we argue that similar constraints must apply for more general compactifications.
Measurement of cold nuclear matter effects for inclusive J/ψ in p+Au collisions at sNN=200 GeV (2022)

Measurement by the STAR experiment at RHIC of the cold nuclear matter (CNM) effects experienced by inclusive J/ψ at mid-rapidity in 0-100% p+Au collisions at sNN = 200 GeV is presented. Such effects are quantified utilizing the nuclear modification factor, RpAu, obtained by taking a ratio of J/ψ yield in p+Au collisions to that in p+p collisions scaled by the number of binary nucleon-nucleon collisions. The differential J/ψ yield in both p+p and p+Au collisions is measured through the dimuon decay channel, taking advantage of the trigger capability provided by the Muon Telescope Detector in the RHIC 2015 run. Consequently, the J/ψ RpAu is derived within the transverse momentum (pT) range of 0 to 10 GeV/c. A suppression of approximately 30% is observed for pT<2 GeV/c, while J/ψ RpAu becomes compatible with unity for pT greater than 3 GeV/c, indicating the J/ψ yield is minimally affected by the CNM effects at high pT. Comparison to a similar measurement from 0-20% central Au+Au collisions reveals that the observed strong J/ψ suppression above 3 GeV/c is mostly due to the hot medium effects, providing strong evidence for the formation of the quark-gluon plasma in these collisions. Several model calculations show qualitative agreement with the measured J/ψ RpAu, while their agreement with the J/ψ yields in p+p and p+Au collisions is worse.
Transformation of Aspergillus parasiticus with a homologous gene (pyrG) involved in pyrimidine biosynthesis (1990)

The lack of efficient transformation methods for aflatoxigenic Aspergillus parasiticus has been a major constraint for the study of aflatoxin biosynthesis at the genetic level. A transformation system with efficiencies of 30 to 50 stable transformants per microgram of DNA was developed for A. parasiticus by using the homologous pyrG gene. The pyrG gene from A. parasiticus was isolated by in situ plaque hybridization of a lambda genomic DNA library. Uridine auxotrophs of A. parasiticus ATCC 36537, a mutant blocked in aflatoxin biosynthesis, were isolated by selection on 5-fluoroorotic acid following nitrosoguanidine mutagenesis. Isolates with mutations in the pyrG gene resulting in elimination of orotidine monophosphate (OMP) decarboxylase activity were detected by assaying cell extracts for their ability to convert [14C]OMP to [14C]UMP. Transformation of A. parasiticus pyrG protoplasts with the homologous pyrG gene restored the fungal cells to prototrophy. Enzymatic analysis of cell extracts of transformant clones demonstrated that these extracts had the ability to convert [14C]OMP to [14C]UMP. Southern analysis of DNA purified from transformant clones indicated that both pUC19 vector sequences and pyrG sequences were integrated into the genome. The development of this pyrG transformation system should allow cloning of the aflatoxin-biosynthetic genes, which will be useful in studying the regulation of aflatoxin biosynthesis and may ultimately provide a means for controlling aflatoxin production in the field.
The Role of Mass Transport on Anisotropic Electrochemical Pattern Etching (1988)

Undercutting during high‐rate electrochemical dissolution of partially masked copper surfaces in the presence of a flowing solution was studied. The electrode geometry consisted of a rectangular cavity with inert sidewalls and an active base, and with aspect ratios (width/depth) between 0.75 and 10. It was found experimentally that undercutting could be suppressed by the combined effect of surface film precipitation and by proper exploitation of convective flow eddies in corners. Under such conditions, the surface film formed preferentially in the corner regions and served therefore to stifle dissolution rates in the local area where undercutting occurs. For the conditions under study, a finite element method was used to calculate hydrodynamic patterns and concentration fields from which both local and overall convective mass transfer coefficients were calculated. The predicted overall mass transfer coefficient was found to agree within 6% of experimental measurements made by the electrochemical limiting current method. General conditions for achieving anisotropic pattern generation were identified.
Investigation the Effect of B Dot Probe Positions in 500kJ Pulsed Power Supply System using MATLAB Simulation (2017)

In a rail gun a small sensing coil named B dot probe is kept over the path of armature which generates the signal from an induced voltage based on faraday's law. The output signal which is generated from the B dot probes consist of a positive and negative elements. The zero-crossing point in the output signal is hypothetical to be the time of passage for the centroid of the armature current, and the zero-crossing times from different probes kept along the length of the rails are on the whole employed to find out the velocity of the projectile. Pulsed power supply system has got a significant role in rail gun system as it gives an enormous electrical energy in a short duration of time to accelerate the movable armature with higher velocity. Pulsed power supply system which is generally capacitor based are the most well-known form of pulsed power supplies system used in rail gun investigation for the past several years. In India for surface fire support, 500-kJ capacitor module pulsed power system design which is capable to accelerate the projectile with a velocity of 1km/s to 1.5km/s, is currently under investigation. In this paper an effort is made to design a 500kJ PPS using MATLAB in order to predetermine the gun parameters such as acceleration of the projectile, muzzle velocity, peak current, current at exit, and also effective barrel length. In general the capacitors are grouped into modules and they are triggered at different time to get desired parameters of rail gun. In this work the capacitors are grouped in five modules and modules are triggered by using projectile positions and projectile position is being identified by using B dot probes positions.
Mass spectrometric analysis of Klebsiella pneumoniae ssp. pneumoniae rough strain R20 (O1− : K20−) lipopolysaccharide preparations: identification of novel core oligosaccharide components and three 3-deoxy-D-manno-oct-2-ulopyranosonic artifacts (1999)

In an attempt to find the best approach for the mass spectrometric analysis of the whole range of lipopolysaccharide (LPS) structures from Klebsiella pneumoniae ssp. pneumoniae rough strain R20 (O1− : K20−), various methods of LPS preparation were applied and the products were analyzed using a range of mass spectrometric techniques. The most productive approach proved to be the removal of lipid A by mild acid hydrolysis and the study of the core oligosaccharide structures using nanoelectrospray time-of-flight mass spectrometry (TOF-MS) in combination with collision-induced dissociation tandem mass spectrometry. This procedure is very sensitive, but results in the generation of a reducing 3-deoxy-D-manno-oct-2-ulopyranosonic acid residue (Kdo) that is susceptible to the formation of artifacts, which give rise to pseudomolecular ions 18, 46, and 88 Da below the pseudomolecular ion for the unmodified species. Alternatively, matrix-assisted laser desorption/ionization TOF-MS combined with post-source decay can be used to study the de- O-acylated LPS preparation and especially to identify those residues bearing phosphate groups and the residues involved in the linkage between the core and lipid A. In addition to the five LPS core structures defined using NMR spectroscopy by Süsskind et al., several extra related LPS structures were identified. Larger LPS species were observed, which surprisingly do not represent species containing longer versions of the novel Klebsiella heptoglycan, but instead are species having the defined core and heptoglycan extended with up to three extra hexuronic acid and one or two extra hexose residues. Copyright © 1999 John Wiley & Sons, Ltd.
Genomic scan for genes affecting body composition before and after training in Caucasians from HERITAGE (2001)

An autosomal genomewide search for genes related to body composition and its changes after a 20-wk endurance-exercise training program has been completed in the HERITAGE Family Study. Phenotypes included body mass index (BMI), sum of eight skinfold thicknesses, fat mass (FM), fat-free mass, percent body fat (%Fat), and plasma leptin levels. A maximum of 364 sib-pairs from 99 Caucasian families was studied with the use of 344 markers with single-point and multipoint linkage analyses. Evidence of significant linkage was observed for changes in fat-free mass with the S100A and the insulin-like growth factor I genes (P = 0.0001). Suggestive evidence (2.0 < or = Lod < 3.0; 0.0001 < P < or = 0.001) was also observed for the changes in FM and %Fat at 1q31 and 18q21-q23, in %Fat with the uncoupling protein 2 and 3 genes, and in BMI at 5q14-q21. At baseline, suggestive evidence was observed for BMI at 8q23-q24, 10p15, and 14q11; for FM at 14q11; and for plasma leptin levels with the low-density lipoprotein receptor gene. This is the first genomic scan on genes involved in exercise-training-induced changes in body composition that could provide information on the determinants of weight loss.
Genetic analyses of Roundabout (ROBO) axon guidance receptors in autism (2008)

Autism is a pervasive developmental disorder diagnosed in early childhood. Abnormalities of serotonergic neurotransmission have been reported in autism. Serotonin transporter (SERT) modulates serotonin levels, and is a major therapeutic target in autism. Factors that regulate SERT expression might be implicated in the pathophysiology of autism. One candidate SERT regulatory protein is the roundabout axon guidance molecule, ROBO. SerT expression in Drosophila is regulated by robo; it plays a vital role in mammalian neurodevelopment also. Here, we examined the associations of ROBO3 and ROBO4 with autism, in a trio association study using DNA from 252 families recruited to AGRE. Four SNPs of ROBO3 (rs3923890, P = 0.023; rs7925879, P = 0.017; rs4606490, P = 0.033; and rs3802905, P = 0.049) and a single SNP of ROBO4 (rs6590109, P = 0.009) showed associations with autism; the A/A genotype of rs3923890 showed lower ADI-R_A scores, which reflect social interaction. Significant haplotype associations were also observed for ROBO3 and ROBO4. We further compared the mRNA expressions of ROBO1, ROBO2, ROBO3, and ROBO4 in the lymphocytes of 19 drug-naïve autistic patients and 20 age- and sex-matched controls. Expressions of ROBO1 (P = 0.018) and ROBO2 (P = 0.023) were significantly reduced in the autistic group; the possibility of using the altered expressions of ROBO as peripheral markers for autism, may be explored. In conclusion, we suggest a possible role of ROBO in the pathogenesis of autism. Abnormalities of ROBO may lead to autism either by interfering with serotonergic system, or by disrupting neurodevelopment. To the best of our knowledge, this is the first report relating ROBO with autism.