gebhart/patrepeval huggingface dataset:
Molecular Genetics of Neuroendocrine Tumors (2018)

Genome-based medicine in oncology allows the development of clinical management strategies tailored to each individual. This approach requires knowledge of the genetic and epigenetic changes that drive tumorigenesis. Low-grade pancreatic neuroendocrine tumors (PanNET) and high-grade neuroendocrine carcinomas (NEC) are overall rare; however, when they develop, they are lethal neoplasms of the pancreas. Recent, comprehensive sequencing efforts have revealed the genetic landscape of PanNET. The driver genes mutated in PanNET are distinct from those altered in other pancreatic neoplasms. The most commonly mutated genes affect the epigenetic state and remodeling of chromatin, and also the telomeric structure. The latter finding established a strong correlation between mutations in alpha-thalassemia/mental retardation X-linked (ATRX) and death domain-associated protein (DAXX) genes and alternative lengthening of telomeres (ALT), a phenotype specific to tumor cells. This correlation was later extended to all tumor types that have the ALT phenotype. The most commonly mutated gene in sporadic PanNET is MEN1 and PanNET associated with hereditary syndromes are most common in patients with multiple endocrine neoplasia type 1 (MEN1) caused by germline mutations in the MEN1 tumor suppressor gene. A subset of PanNET has genetic and epigenetic changes in genes that are part of the mammalian target of rapamycin (mTOR) pathway, suggesting that patients that benefited from therapies utilizing mTOR inhibitors had PanNET with activated mTOR pathway. High-grade NEC, by contrast, are characterized by genetic alterations in the RB1 and TP53 genes. The elucidation of genetic alterations underlying PanNET and NEC tumorigenesis provides new opportunities to identify targets with potential prognostic value and intracellular processes that can be exploited therapeutically.
Evaluation of Fluence Correction Algorithms in Multispectral Photoacoustic Imaging (2020)

Multispectral photoacoustic imaging (MPAI) is a promising emerging diagnostic technology, but fluence artifacts can degrade device performance. Our goal was to develop well-validated phantom-based test methods for evaluating and comparing MPAI fluence correction algorithms, including a heuristic diffusion approximation, Monte Carlo simulations, and an algorithm we developed based on novel application of the diffusion dipole model (DDM). Phantoms simulated a range of breast-mimicking optical properties and contained channels filled with chromophore solutions (ink, hemoglobin, or copper sulfate) or connected to a previously developed blood flow circuit providing tunable oxygen saturation (SO<sub>2</sub>). The DDM algorithm achieved similar spectral recovery and SO<sub>2</sub> measurement accuracy to Monte Carlo-based corrections with lower computational cost, potentially providing an accurate, real-time correction approach. Algorithms were sensitive to optical property uncertainty, but error was minimized by matching phantom albedo. The developed test methods may provide a foundation for standardized assessment of MPAI fluence correction algorithm performance.
Synthesis of polylactide with varying molecular weight and aliphatic content: Effect on moisture sorption (2010)

Abstract Polylactide (PLA) is a bio‐based, biodegradable polymer, which is derived from lactic acid and has numerous potential applications, some of which are limited by its moisture barrier and thermal properties. Prior studies have been inconsistent about how moisture sorption in PLA varies with crystallinity and molecular weight. This research is a systematic study of how moisture sorption in PLA depends on molecular weight and aliphatic content via end‐group modification. PLA with varying aliphatic content was synthesized by ring‐opening polymerization of L ‐lactide initiated with different long‐chain aliphatic alcohols. The terminating end groups were also modified from hydroxyl to acetoxy to eliminate hydrophilic end groups. Molecular weight was controlled by varying the ratio of L ‐lactide monomer to alcohol initiator, and triethylaluminum was used as the catalyst for precise control over molecular weight. The molecular weight and end‐group compositions were verified by gel permeation chromatography and nuclear magnetic resonance. Moisture sorption of the modified PLA samples was measured with a quartz crystal microbalance. Quartz crystal microbalance experiments revealed that both molecular weight and aliphatic content contributed to the sorption properties of PLA. © 2010 Wiley Periodicals, Inc. J Appl Polym Sci, 2011
The Creation of Super-Excited Electronic Feshbach Resonances by EUV-induced Dissociation of O2 (2009)

We resolve complex electron autoionization dynamics in molecules in real time for the first time, where a second electron cannot be ejected from O2 until the internuclear separation of the fragments is &gt;30Å.
Additional file 1: Figure S1. of Gastrointestinal delivery of propofol from fospropofol: its bioavailability and activity in rodents and human volunteers (2015)

Absolute latency of ipsilateral paw in CCI rats before and after fospropofol or vehicle treatment.
Enhancement of enzymatic activity for myoglobins by modification of heme-propionate side chains (2004)

The modification of myoglobin is an attractive process not only for understanding its molecular mechanism but also for engineering the protein function. The strategy of myoglobin functionalization can be divided into at least two approaches: site-directed mutagenesis and reconstitution with a non-natural prosthetic group. The former method enables us to mainly modulate the physiological function, while the latter has the advantage of introducing a new function on the protein. Particularly, replacement of the native hemin with an artificially created hemin having hydrophobic moieties at the terminal of the heme-propionate side chains serves as an appropriate substrate-binding site near the heme pocket, and consequently enhances the peroxidase and peroxygenase activities for the reconstituted myoglobin. In addition, the incorporation of the synthetic hemin bearing modified heme-propionates into an appropriate apomyoglobin mutant drastically enhances the peroxidase activity. In contrast, to convert myoglobin into a cytochrome P450 enzyme, a flavin moiety as an electron transfer mediator was introduced at the terminal of the heme-propionate side chain. The flavomyoglobin catalyzes the deformylation of 2-phenylpropanal in the presence of NADH under aerobic conditions through the peroxoanion formation from the oxygenated species. In addition, modification of the heme-propionate side chains has an significant influence on regulating the reactivity of the horseradish peroxidase. Furthermore, the heme-propionate side chain can form a metal binding site with a carboxylate residue in the heme pocket. These studies indicate that modification of the heme-propionate side chains can be a new and effective way to engineer functions for the hemoproteins.
Studying the effect of AI Code Generators on Supporting Novice Learners in Introductory Programming (2023)

AI code generators like OpenAI Codex have the potential to assist novice programmers by generating code from natural language descriptions, however, over-reliance might negatively impact learning and retention. To explore the implications that AI code generators have on introductory programming, we conducted a controlled experiment with 69 novices (ages 10-17). Learners worked on 45 Python code-authoring tasks, for which half of the learners had access to Codex, each followed by a code-modification task. Our results show that using Codex significantly increased code-authoring performance (1.15x increased completion rate and 1.8x higher scores) while not decreasing performance on manual code-modification tasks. Additionally, learners with access to Codex during the training phase performed slightly better on the evaluation post-tests conducted one week later, although this difference did not reach statistical significance. Of interest, learners with higher Scratch pre-test scores performed significantly better on retention post-tests, if they had prior access to Codex.
Label-Free Colorimetric Nanobiosensor for Nucleic Acid Detection Based on Peroxidase Mimicking Activity of Magnetic Nanoparticles (2011)

Colorimetric detection of nucleic acids has attracted considerable research attention due to many advantages as compared to the conventional gel based assays, such as rapid visual detection, low cost and easy implementation to point-of-care testing (POCT) facilities. Along this line, we developed a new and simple label-free colorimetric detection method of target DNA utilizing the peroxidase mimicking activity of magnetic nanoparticles (MNPs), which relies on the target DNA-induced shielding action against the peroxidase activity. PCRamplified sample solution is mixed with unmodified MNPs followed by addition of colorimetric reaction solution containing colorimetric substrates and hydrogen peroxidase (H2O2). In the presence of target DNA, the am plified DNA products diminished the accessibility of positively charged substrate, OPD toward MNPs in a supernatant and the direct contact of the substrate with MNPs by adsorbing onto the surface of MNPs through electrostatic interactions. This simple but very efficient colorimetric strategy was successfully demonstrated by correctly diagnosing Chlamydia infection using a real human urine sample. Since the results can be clearly seen by the naked eye without any sophisticated instrumentation, this method has great potential as a POCT sensor for the verification of the amplified nucleic acids.
Handling Noisy Queries in Cross Language FAQ Retrieval (2010)

Recent times have seen a tremendous growth in mobile based data services that allow people to use Short Message Service (SMS) to access these data services. In a multilingual society it is essential that data services that were developed for a specific language be made accessible through other local languages also. In this paper, we present a service that allows a user to query a Frequently-Asked-Questions (FAQ) database built in a local language (Hindi) using Noisy SMS English queries. The inherent noise in the SMS queries, along with the language mismatch makes this a challenging problem. We handle these two problems by formulating the query similarity over FAQ questions as a combinatorial search problem where the search space consists of combinations of dictionary variations of the noisy query and its top-N translations. We demonstrate the effectiveness of our approach on a real-life dataset.
Quantitative modeling predicts mechanistic links between pre-treatment microbiome composition and metronidazole efficacy in bacterial vaginosis (2020)

Bacterial vaginosis is a condition associated with adverse reproductive outcomes and characterized by a shift from a Lactobacillus-dominant vaginal microbiota to a polymicrobial microbiota, consistently colonized by strains of Gardnerella vaginalis. Metronidazole is the first-line treatment; however, treatment failure and recurrence rates remain high. To understand complex interactions between Gardnerella vaginalis and Lactobacillus involved in efficacy, here we develop an ordinary differential equation model that predicts bacterial growth as a function of metronidazole uptake, sensitivity, and metabolism. The model shows that a critical factor in efficacy is Lactobacillus sequestration of metronidazole, and efficacy decreases when the relative abundance of Lactobacillus is higher pre-treatment. We validate results in Gardnerella and Lactobacillus co-cultures, and in two clinical cohorts, finding women with recurrence have significantly higher pre-treatment levels of Lactobacillus relative to bacterial vaginosis-associated bacteria. Overall results provide mechanistic insight into how personalized differences in microbial communities influence vaginal antibiotic efficacy.
Supplementary Figure 6 from Collaboration of Kras and Androgen Receptor Signaling Stimulates EZH2 Expression and Tumor-Propagating Cells in Prostate Cancer (2023)

&lt;p&gt;PDF file, 91K, Sphere formation of normal primary prostate cells is suppressed by DZNep.&lt;/p&gt;
Adenovirus-mediated transfer of a human dystrophin gene to skeletal muscle of mdx mouse. (1994)

Due to their quiescent nature and spatial complexity, many target tissues for gene therapy will require novel strategies. An alternative to ex vivo gene transfer, providing many technical advantages and possibly allowing sufficient transfer of the therapeutic gene, is direct in vivo delivery of the vehicle. For a favorable outcome, this procedure is dependent on a high-titer vector, fully competent before post-mitotic cells. In view of the restrictions with the use of retroviruses, we investigated the potentials of adenovirus. Adenoviruses have as primary targets of infection the differentiated epithelial cell. The large DNA genome of the virus hints to a large cloning capacity. Furthermore, the wild type adenovirus has been largely used in man as a vaccine against adenovirus-induced respiratory disease. Taken together, the biological characteristics of adenovirus and the precedent of administration to humans are suggestive of adenovirus-based gene therapy for diseases involving a variety of quiescent tissues. The use of a replication-defective adenovirus carrying a gene encoding a nuclearly-targeted beta-galactosidase Ad.RSV beta gal demonstrated that replication-defective adenovirus offers an efficient means to transfer a gene for extended periods of time in the liver, muscle, lung and brain (1-6).
Shape Control of Nanostructures in Na doped PbTe-PbS system (2012)

Extended abstract of a paper presented at Microscopy and Microanalysis 2012 in Phoenix, Arizona, USA, July 29 – August 2, 2012.
Breaking Down the Barriers: Improving Asian Access to Social Rented Housing (2001)

The title of this report reflects the importance of the issues it raises for the broader debate about tackling social exclusion. The study aims to discover whether there are barriers inhibiting access to social housing by South Asian households in Bradford and how they might be removed. It is particularly timely given the recent strengthening of the Race Relations Act 1976, and the introduction of the Human Rights Act. Both these developments will have a direct impact on the ways in which local authorities and housing associations operate, by making the differential impact of policies and practices on various communities a matter for investigation and action. These developments make the study relevant to the many cities which have substantial minority ethnic communities. At the time of publication, the summer of 2001, it is also highly topical because of the publicity which has followed violent incidents in some northern cities which allegedly had a racial dimension.
Impact of 3D integration on 7nm high mobility channel devices operating in the ballistic regime (2014)

We report for the first time the impact of 3D IC process induced local thermo-mechanical stress effects on CMOS devices for 7nm technology node (N7) operating in the ballistic regime. We show that the ballistic current is less affected by the uniaxial stress than the drift current. The ballistic current ratio decreases for longer gate, it is 80%, 45% of the total current for respectively 14nm and 40nm gate lengths devices resulting in larger TSV proximity effects for longer devices. 4 point bending measurements for Ge channel p-FinFETs, confirm the simulated stress sensitivities used to provide a physical estimation of the Keep Out Zone (KOZ). For high mobility channel devices, whereas N7 p-FinFETs exhibits similar TSV stress sensitivities, the KOZ for n-FinFETs is a function of the channel material choice for the co-integration. Unstrained Ge n-FinFETs are largely affected by the TSV proximity, 40% more than Si, SiGe and strained Ge n-FinFETs. Materials like Ge and InGaAs have a reduced sensitivity to the vertical stress component whereas the impact is significant in the case of Si and SiGe n-type devices, with more than 10% change in drive current for 400MPa compressive vertical stress.
Mitochondria, Energetics, Epigenetics, and Cellular Responses to Stress (2014)

Understanding mitochondria-cell signaling will provide insight into individual responses to environmental hazards, improving prediction of hazard and susceptibility to environmental stressors.
Adjuvant Autologous Melanoma Vaccine for Macroscopic Stage III Disease: Survival, Biomarkers, and Improved Response to CTLA-4 Blockade (2016)

Background. There is not yet an agreed adjuvant treatment for melanoma patients with American Joint Committee on Cancer stages III B and C. We report administration of an autologous melanoma vaccine to prevent disease recurrence. Patients and Methods. 126 patients received eight doses of irradiated autologous melanoma cells conjugated to dinitrophenyl and mixed with BCG. Delayed type hypersensitivity (DTH) response to unmodified melanoma cells was determined on the vaccine days 5 and 8. Gene expression analysis was performed on 35 tumors from patients with good or poor survival. Results. Median overall survival was 88 months with a 5-year survival of 54%. Patients attaining a strong DTH response had a significantly better (p = 0.0001) 5-year overall survival of 75% compared with 44% in patients without a strong response. Gene expression array linked a 50-gene signature to prognosis, including a cluster of four cancer testis antigens: CTAG2 (NY-ESO-2), MAGEA1, SSX1, and SSX4. Thirty-five patients, who received an autologous vaccine, followed by ipilimumab for progressive disease, had a significantly improved 3-year survival of 46% compared with 19% in nonvaccinated patients treated with ipilimumab alone (p = 0.007). Conclusion. Improved survival in patients attaining a strong DTH and increased response rate with subsequent ipilimumab suggests that the autologous vaccine confers protective immunity.
Patellar Tilt and Subluxation in Total Knee Arthroplasty (1993)

Two hundred thirty-four primary total knee prostheses were evaluated with a 45 degrees merchant view to examine patellar position and fixation. Despite a standardized technique for obtaining roentgenographs, patellar position varied with leg position. Overall, 54.7% tracked centrally, 31.2% tilted, and 14.5% displaced. The incidence of these findings was the same whether the patella was domed or congruent. Neither pain scores nor fixation were affected by position. Postoperative tilt and displacement were more common in patellae that were tilted preoperatively. The incidence of postoperative tilt or displacement was not significantly different in knees in which a lateral release was performed. Patellar tilt in some patients seems inevitable despite careful technique because intraoperative tests are static and postoperative function is dynamic. This does not bode well for wear in a metal-backed patella. Tilt caused increased loading at the periphery of the component where most metal-backed prostheses have thin polyethylene.
Faculty Opinions recommendation of Acetylation targets the M2 isoform of pyruvate kinase for degradation through chaperone-mediated autophagy and promotes tumor growth. (2011)

Read the full review for this Faculty Opinions recommended article: Acetylation targets the M2 isoform of pyruvate kinase for degradation through chaperone-mediated autophagy and promotes tumor growth.
Characterization of mixed-signal properties of MOSFETs with high-k (SiON/HfSiON/TaN) gate stacks (2006)

The correlation between the stoichiometry of HfSiON gate dielectrics and mixed-signal properties of low-power MOSFETs is investigated. MOSFETs with gate length L down to 100 nm were fabricated in a conventional fabrication flow with a thermal budget of 1000/spl deg/C. The equivalent oxide thickness values of the gate stacks ranged from 12.0 to 14.4 /spl Aring/. The inversion thickness t/sub ox//sup inv/ ranged between 16.2 and 18.9 /spl Aring/. Accumulation leakage current density at V/sub g/=V/sub fb/-1 V ranged from 3.1/spl times/10/sup -3/ to 3.9/spl times/10/sup -2/ A/spl middot/cm/sup -2/, corresponding to a leakage reduction of around 1000 times compared with that of SiON/TaN. The inversion leakage current density at V/sub g/=V/sub t/+0.7 V was found to be between 0.18 and 0.66 A/spl middot/cm/sup -2/, i.e., 20 times lower than that of SiON/TaN. The threshold voltage instability (/spl Delta/V/sub t/) of the high-k gate stacks was found to be below 10 mV, corresponding to a (bulk) oxide trap density N/sub ot/<3/spl times/10/sup 10/ cm/sup -2/. Normalized input-referred gate noise spectra S/sub vg/ showed minor dependence on the Hf content of the gate dielectric. This is attributed to the fact that the main sources for the low-frequency (LF) 1/f noise are defects located at the interfaces rather than bulk defects in the gate dielectric. Moderate high- and low-field mobilities of 50%-70% of a SiON/TaN reference device were found in MOSFETs with Hf-based gate dielectric. Of the investigated layers, stoichiometric (55% Hf) and Hf-rich (70% Hf) silicates on SiO/sub 2/ interface show the best compromise in terms of gate leakage reduction, threshold voltage instability, LF noise, drive current, and analog voltage gain. For an HfSiON silicate dielectric layer with 70% Hf and SiO/sub 2/ interface, a low-field peak electron mobility /spl mu//sub eff/=148 cm/sup 2//V/spl middot/s, an oxide trap density N/sub ot/<1.4/spl times/10/sup 10/ cm/sup -2/, and a drive current I/sub ON/=459 /spl mu/A//spl mu/m at I/sub OFF/=9 pA//spl mu/m were found. The analog voltage gain A/sub v/ of a MOSFET with this gate dielectric and W/L=1/0.45 was found to be A/sub v/=121. To meet specifications for mixed-signal properties, optimization of dopant engineering along with tuning of the gate stack properties is required to improve the performance of high-k-based MOSFETs.
Exogenous Ouabain Is Accumulated in the Adrenals and Mimics the Kinetics of Endogenous Digitalis-like Factor in Rats. (1998)

Ouabain has been isolated as an endogenous pathogenetic factor in salt-induced hypertension and has been shown to be rich in the adrenals. In this study, organ accumulation of orally administered [3H]ouabain was examined in rats. Exogenous [3H]ouabain was accumulated in high levels in the adrenals, especially in the zona intermedia, and was not metabolized in the rat. Accumulated [3H]ouabain mimicked the movement of "endogenous" digitalis-like factor, since 1) the plasma [3H]ouabain level decreased in bilaterally adrenalectomized rats, 2) the plasma [3H]ouabain level increased accompanied by a decrease in [3H]ouabain content in the adrenals in reduced renal mass hypertensive rats, and 3) [3H]ouabain levels in plasma and in the adrenals increased in spontaneously hypertensive rats, as compared with those in respective control animals. Moreover, the rat diet contained a relatively high amount of ouabain-like immunoreactivity (OLI), and the ratio of the [3H]ouabain content to OLI in each organ was comparable to that of the daily intake of dietary [3H]ouabain to OLI. Furthermore, high 3H-radioactivities were also observed in the adrenals of rats that ingested [3H]digoxin and [3H]digitoxin. These data suggest that exogenous ouabain, related cardiotonic glycosides of plant origin, or both accumulate in the adrenals and, at least in part, act as "endogenous" digitalis-like factor(s).