gebhart/patrepeval huggingface dataset:
Methylated DNA markers in urine aid in the selective identification of patients with prostate cancer as well as clinically significant pathology. (2022)

5091 Background: Controversy surrounding prostate-specific antigen (PSA) based screening for prostate cancer (PCa) highlights the need for non-invasive assays that better discriminate patients with and without clinically significant prostate cancer (csPCa). Such distinction avoids overtreatment in patients with absent or indolent disease while capturing pathology that would derive benefit from intervention. We analyzed the presence of specific methylated DNA markers (MDMs) within urine samples of patients with biopsy proven PCa and assessed the ability to discriminate these patients from healthy controls with no clinical suspicion for PCa. Methods: 24 healthy volunteers with no clinical suspicion for PCa were age-matched to 24 patients with biopsy-confirmed disease across all Gleason scores. Urine collected from subjects was centrifuged with the cell-free supernatant analyzed in a blinded fashion for methylation signal within specific DNA sequences across 14 genes ( HES5, ZNF655, ITPRIPL1, MAX.chr3.193, SLCO3A1, CHST11, SERPINB9, WNT3A, KCNB2, GAS6, AKR1B1, MAX.chr3.727, GRASP, ST6GALNAC2) by target enrichment long-probe quantitative-amplified signal assays. A patient was considered to have a positive MDM panel if any individual marker exceeded the corresponding100% specificity cut-off value (overall MDM panel specificity of 100%). MDM panel positivity was used to evaluate the sensitivity for distinguishing patients with PCa (any Gleason score) from controls as well as discriminate csPCa cancers from PCa Gleason 6. Results: Median age of healthy controls and PCa patients was 70 years (IQR 67-72) and 65 years (IQR 61-71), respectively. Median PSA was 6.4 (IQR 4.9-9.0) among PCa patients, including median PSA of 5 (IQR 4.0-6.1) for Gleason 6, and 7.8 (IQR 5.1-9.2) for Gleason ≥7 disease. Gleason 6, Gleason 7, and Gleason 8+ cancer was noted in 8, 10, and 6 patients, respectively. Utilizing an overall specificity cut-off of 100% for discriminating normal controls from PCa cases across the MDM panel revealed an overall sensitivity of 83% (95% CI: 63-95%) for detection of PCa (6 of 8 Gleason 6, 9 of 10 Gleason 7, 5 of 6 Gleason 8+) and 88% (95% CI: 62-98%) for csPCa (Gleason ≥ 7). When considering a 100% specificity threshold for controls and Gleason 6 patients, the sensitivity the MDM panel was 69% (95% CI: 41-89%) for csPCa (6 of 10 Gleason 7, 5 of 6 Gleason 8+). Conclusions: We describe a panel of 14 MDMs within urine that offer high specificity and sensitivity for detection of prostate cancers as well as selective identification of clinically significant disease states. Prospective comparison between urine MDMs and PSA blood testing is necessary to discern the differential clinical impact of each screening methodology.
Interleukin 18 in acute myocardial infarction (2000)

Interleukin 18 (IL-18), which is a recently cloned cytokine synthesised by Kupffer cells, has been shown to activate macrophages.1 Macrophages and T cells have been reported to be activated in patients with acute myocardial infarction (MI).2 IL-18 is postulated to play a role in the development of myocardial dysfunction through activation of immune cells. However, the circulating concentration of IL-18 has not been reported in patients with acute MI.

To elucidate the changes in the release of IL-18 in patients with coronary artery disease, we examined the correlation between IL-18 concentrations and the serum activities of myocardial enzymes, estimating myocardial necrosis or atrial natriuretic peptide (ANP). Our goal was to determine whether measurement of IL-18 could be used as a new indicator of myocardial damage in patients with acute MI.

We evaluated 24 patients with acute MI (19 men and five women aged 39–79 years). …
Prevention of hepatitis C virus infection using a broad cross‐neutralizing monoclonal antibody (AR4A) and epigallocatechin gallate (2015)

The anti-hepatitis C virus (HCV) activity of a novel monoclonal antibody (mAb; AR4A) and epigallocatechin gallate (EGCG) were studied in vitro using a HCV cell culture system and in vivo using a humanized liver mouse model capable of supporting HCV replication. Alone, both exhibit reliable cross-genotype HCV inhibition in vitro, and combination therapy completely prevented HCV infection. In vitro AR4A mAb (alone and combined with EGCG) robustly protects against the establishment of HCV genotype 1a infection. EGCG alone fails to reliably protect against an HCV challenge. In conclusion, AR4A mAb represents a safe and efficacious broadly neutralizing antibody against HCV applicable to strategies to safely prevent HCV reinfection following liver transplantation, and it lends further support to the concept of HCV vaccine development. The poor bioavailability of EGCG limits HCV antiviral activity in vitro.
Carrier Transport Mechanism of Pd/Pt/Au Ohmic Contacts to p-GaN in InGaN Laser Diode (2002)

The dependence of contact resistivity on the carrier concentration for the non-alloyed Pd contacts on p-GaN and the temperature dependence measurements of sheet resistivity of p-GaN suggest that carrier transport at the interface between the contact and the p-GaN would be dominated by deep level defect band, rather than the valence band. Based on these results, in order to reduce the operating voltage of the InGaN laser diode (LD), we designed a p-GaN : Mg contact layer, where the ohmic metals are contacted, and optimized the p-GaN contact layer.
Delta Wing Stall and Roll Control Using Segmented Piezoelectric Fluidic Actuators (2005)

The separated flow around a balance-mounted, 60-deg sweptback, semispan delta wing with a sharp leading edge was controlled using zero-mass-flux periodic excitation from a segmented leading-edge slot. Excitation was generated by cavity-installed piezoelectric actuators operating at resonance with amplitude modulation (AM) and burst mode (BM) signals being used to achieve reduced frequencies (scaled with the freestream velocity and the root chord) in the range from O(1) to O(10). Results of a parametric investigation, studying the effects of AM frequency, BM duty cycle and frequency, excitation amplitude, location of the actuation along the leading edge, and optimal phase difference between the actuators, as well as the Reynolds number, are reported and discussed
Efficient rate-distortion optimized mode selection of H.264/AVC intra coding (2011)

Rate-distortion optimization (RDO) can significantly improves encoder performance in H.264-like video coding applications. In H.264/AVC, rate-distortion optimization (RDO) method has to code the video by exhaustively trying all the mode combinations including the different intra- and inter-prediction modes. Therefore, the complexity and computation load of video coding in H.264/AVC increase drastically compared to any previous standards. This paper reviewed the conventional fast cost functions of the intra encoder and proposed an enhanced low complex cost function for H.264/AVC intra 4×4 mode selections. The enhanced cost function uses sum of absolute Hadamard-transformed differences (SATD) and mean absolute deviation of the residual block to estimate distortion part of the cost function. A threshold based large coefficients count is also used for estimating the bit-rate part. The proposed method improves the rate-distortion performance of the conventional fast cost functions while maintaining low complexity requirement. As the results, the encoding process can be significantly accelerated with use of the proposed cost function. Simulation results confirmed that the proposed method reduced about 85% of computation of original encoder with negligible rate-distortion performance degradation.
A Study on the Effects of Release Area on the Quality Factor of Contour-Mode Resonators by Laser Doppler Vibrometry (2017)

Through the use of a laser Doppler vibrometer, it is shown that a 31% variation in quality factor can occur due to the effect of undercutting of the device layers outside of the anchors of a 220-MHz aluminum nitride contour-mode resonator. This undercutting is a result of the isotropic etch process used to release the device from the substrate. This paper shows that the variation in Q is a function of the release distance, L , between the active region of the resonator and the edge of this released region. This paper also determined a design modification that eliminated this issue and achieved a Q of 3048, which is independent of L .
Product-Form Poisson-Like Distributions and Complex Balanced Reaction Systems (2016)

Stochastic reaction networks are dynamical models of biochemical reaction systems and form a particular class of continuous-time Markov chains on $\mathbb{N}^n$. Here we provide a fundamental characterization that connects structural properties of a network to its dynamical features. Specifically, we define the notion of “stochastically complex balanced systems” in terms of the network's stationary distribution and provide a characterization of stochastically complex balanced systems, parallel to that established in the 1970s and 1980s for deterministic reaction networks. Additionally, we establish that a network is stochastically complex balanced if and only if an associated deterministic network is complex balanced (in the deterministic sense), thereby proving a strong link between the theory of stochastic and deterministic networks. Further, we prove a stochastic version of the “deficiency zero theorem” and show that any (not only complex balanced) deficiency zero reaction network has a product-form Poisson-like stationary distribution on all irreducible components. Finally, we provide sufficient conditions for when a product-form Poisson-like distribution on a single (or all) component(s) implies the network is complex balanced, and we explore the possibility to characterize complex balanced systems in terms of product-form Poisson-like stationary distributions.
Identification of the Tirandamycin Biosynthetic Gene Cluster from Streptomyces sp. 307‐9 (2010)

The structurally intriguing bicyclic ketal moiety of tirandamycin is common to several acyl-tetramic acid antibiotics, and is a key determinant of biological activity. We have identified the tirandamycin biosynthetic gene cluster from the environmental marine isolate Streptomyces sp. 307-9, thus providing the first genetic insight into the biosynthesis of this natural product scaffold. Sequence analysis revealed a hybrid polyketide synthase-nonribosomal peptide synthetase gene cluster with a colinear domain organization, which is entirely consistent with the core structure of the tirandamycins. We also identified genes within the cluster that encode candidate tailoring enzymes for elaboration and modification of the bicyclic ketal system. Disruption of tamI, which encodes a presumed cytochrome P450, led to a mutant strain deficient in production of late stage tirandamycins that instead accumulated tirandamycin C, an intermediate devoid of any post assembly-line oxidative modifications.
Response to a Randomized Trial on Mannitol Use During Partial Nephrectomy (2021)

undocumented immigrant patients with end-stage kidney disease should not be precluded from consideration for kidney transplant based on immigration status alone. Additional studies are necessary to identify those at risk of dropout during follow-up and whether specialized protocols would benefit this unique population to further optimize posttransplant care and outcomes.
Breast Reconstruction Following Nipple-Sparing Mastectomy (2013)

INTRODUCTION: Nipple-sparing mastectomy (NSM) is increasingly used for treatment and prevention of breast cancer. Little data exists on risk factors for complications and reconstruction outcomes. METHODS: Multi-surgeon single institution retrospective review was performed between 2007-2012. RESULTS: Two hundred eighty-five patients underwent 500 nipple-sparing mastectomy procedures for breast cancer (46%) or risk reduction (54%). The average BMI was 24, and 6% were smokers. Procedures were performed utilizing inferolateral inframammary fold (IMF) (51%), periareolar (24%), lateral radial (10%), inferior radial (4%), or pre-existing scar (11%) incisions (Figure 1).Figure 1: Figure 1.Immediate breast reconstruction (reconstruction rate 98.8%) was performed with direct-to-implant (DTI) (59%), tissue expander-implant (38%), or autologous (2%) reconstruction. Seventy-one percent used ADM and 11% mesh. Seventy-seven reconstructions had radiotherapy. Complications included infection (3.3%), skin necrosis (5.2%), nipple necrosis (4.4%), seroma (1.7%), hematoma (1.7%), and implant loss (1.9%). Positive predictors for total complications by multivariate regression analysis included smoking (OR=3.3, C.I.=1.289-8.486) and periareolar incisions (OR=3.63, C.I.=1.850-7.107). Increasing BMI predicted skin necrosis (OR=1.154, C.I.=1.036-1.286) and preoperative radiation predicted nipple necrosis (OR=4.86, C.I.=1.0197-23.169). An IMF incision decreased complications (OR-0.018, C.I.=0.0026-0.12089). An IMF incision and preoperative radiation were associated with more single-stage reconstructions while lateral radial, inferior radial, and smoking were associated with two-stage reconstructions (p<0.05 for each). Five-year trends showed increasing numbers of NSM reconstructions, fewer complications, an increase in IMF and decrease in periareolar incisions, and an increase in single-stage reconstruction (Figure 2). A patient survey showed preference for the IMF incision.Figure 2: Figure 2.CONCLUSION: Nipple-sparing mastectomy and immediate reconstruction has a high rate of success and low rate of complications. The inferolateral IMF incision decreases complications, is preferable to patients, and may allow a greater proportion of direct-to-implant reconstructions. Periareolar incisions increase ischemic-related complications and should be avoided in inexperienced hands. Other risk factors important to assess in deciding operative strategy include patient BMI, smoking status, desired implant volume, and preoperative radiotherapy.
The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications (2005)

The MBT provides a well-organized assortment of core classes that provide a uniform data model for the description of biological structures and automate most common tasks associated with the development of applications in the molecular sciences (data loading, derivation of typical structural information, visualization of sequence and standard structural entities).
Comparison of Mesenchymal Stem Cells (Osteoprogenitors) Harvested From Proximal Humerus and Distal Femur During Arthroscopic Surgery (2013)

Human MSCs derived from concentrated bone marrow aspirate are a promising biological addition that may have practical use in the future of soft tissue augmentation. Arthroscopic techniques for bone marrow aspiration that do not require an additional surgical site for aspiration (e.g., iliac crest) or a second operative procedure may facilitate future use of MSCs in arthroscopic surgery.
Computed tomography of the pulmonary parenchyma. Part 2 (1985)

A series of patients with documented predominantly interstitial pulmonary disease was examined by routine and high-resolution computed tomography (CT) and compared to a series of twenty-one normals. Inspiratory-expiratory lung density measurements were also obtained at predetermined levels. Several basic CT signs of interstitial disease were identified: finely irregular and thickened pleural surfaces; irregular vascular shadows; thickened and irregular bronchial walls making bronchi visible over a longer portion of their course in the lungs; reticular network of lines with three patterns easily distinguishable by the size of their reticular element; hazy patches of increased density of various sizes distinguishable from alveolar filling processes by the fact that vessels can still be visualized through them; and nodules of various sizes. Micronodules are often associated with a small or medium-size reticular network and in most cases seem to represent points of confluence rather than isolated nodules. The hematogenous origin of some nodules can be specifically suggested when feeding vessels are demonstrated on thin-section scans. Nodules associated with a large network of thickened septa are suggestive of lymphangitic carcinomatosis. Inspiratory-expiratory density gradients can be more useful in confirming the diagnosis of interstitial disease than absolute measurements.
Real-World Variability in the Prediction of Intracranial Aneurysm Wall Shear Stress: The 2015 International Aneurysm CFD Challenge (2018)

Wide variability exists in the prediction of intracranial aneurysm WSS. While segmentation and CFD solver techniques may be difficult to standardize across groups, our findings suggest that some of the variability in image-based CFD could be reduced by establishing guidelines for model extents, inflow rates, and blood properties, and by encouraging the reporting of normalized hemodynamic parameters.
Triggering interferon signaling in T cells with avadomide sensitizes CLL to anti-PD-L1/PD-1 immunotherapy (2020)

Cancer treatment has been transformed by checkpoint blockade therapies, with the highest anti-tumor activity of anti-programmed death 1 (PD-1) antibody therapy seen in Hodgkin lymphoma. Disappointingly, response rates have been low in the non-Hodgkin lymphomas, with no activity seen in relapsed/refractory chronic lymphocytic leukemia (CLL) with PD-1 blockade. Thus, identifying more powerful combination therapy is required for these patients. Here, we preclinically demonstrate enhanced anti-CLL activity following combinational therapy with anti-PD-1 or anti-PD-1 ligand (PD-L1) and avadomide, a cereblon E3 ligase modulator (CELMoD). Avadomide induced type I and II interferon (IFN) signaling in patient T cells, triggering a feedforward cascade of reinvigorated T-cell responses. Immune modeling assays demonstrated that avadomide stimulated T-cell activation, chemokine expression, motility and lytic synapses with CLL cells, as well as IFN-inducible feedback inhibition through upregulation of PD-L1. Patient-derived xenograft tumors treated with avadomide were converted to CD8+ T cell-inflamed tumor microenvironments that responded to anti-PD-L1/PD-1-based combination therapy. Notably, clinical analyses showed increased PD-L1 expression on T cells, as well as intratumoral expression of chemokine signaling genes in B-cell malignancy patients receiving avadomide-based therapy. These data illustrate the importance of overcoming a low inflammatory T-cell state to successfully sensitize CLL to checkpoint blockade-based combination therapy.
P‐54: Glass Substrate for LTPS‐TFT with Precisely Controlled Thermal Shrinkage (2016)

Factors for precise control of thermal shrinkage during LTPS‐TFT formation process were investigated. First of all, novel displacement‐measurement apparatus with high accuracy was developed. Using this system, thermal shrinkage behavior was evaluated for commercially produced glass sheet. As a result, it was found that the effect of induced stress in glass sheet forming process cannot be negligible for controlling the thermal shrinkage behavior during LTPS‐TFT formation process.
Constructing candidate word lists using acoustically similar word groups (1992)

A method for identifying a set of candidate words that matches well with a given utterance is discussed. The method uses precomputed groups of acoustically similar words. Given a vocabulary, for each word a short list of words that are acoustically similar to it is computed. These groups are constructed using training utterances recorded by several speakers and used in an isolated utterance recognition system to construct candidate word lists during recognition. Experiments show that the correct word appears on the short list of candidate words constructed during recognition using this scheme over 98% of the time.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Improvement of bovine ß-lactoglobulin production and secretion by Lactococcus lactis (2005)

The stabilizing effects of staphylococcal nuclease (Nuc) and of a synthetic propeptide (LEISSTCDA, hereafter called LEISS) on the production of a model food allergen, bovine beta-lactoglobulin (BLG), in Lactococcus lactis were investigated. The fusion of Nuc to BLG (Nuc-BLG) results in higher production and secretion of the hybrid protein. When LEISS was fused to BLG, the production of the resulting protein LEISS-BLG was only slightly improved compared to the one obtained with Nuc-BLG. However, the secretion of LEISS-BLG was dramatically enhanced (approximately 10- and 4-fold higher than BLG and Nuc-BLG, respectively). Finally, the fusion of LEISS to Nuc-BLG resulting in the protein LEISS-Nuc-BLG led to the highest production of the hybrid protein, estimated at approximately 8 microg/ml (approximately 2-fold higher than Nuc-BLG). In conclusion, the fusions described here led to the improvement of the production and secretion of BLG. These tools will be used to modulate the immune response against BLG via delivery of recombinant lactococci at the mucosal level, in a mouse model of cow's milk allergy.
DFT Computed Dielectric Response and THz Spectra of Organic Co-Crystals and Their Constituent Components (2019)

Terahertz (THz) spectroscopy has been put forth as a non-contact, analytical probe to characterize the intermolecular interactions of biologically active molecules, specifically as a way to understand, better develop, and use active pharmaceutical ingredients. An obstacle towards fully utilizing this technique as a probe is the need to couple features in the THz regions to specific vibrational modes and interactions. One solution is to use density functional theory (DFT) methods to assign specific vibrational modes to signals in the THz region, coupling atomistic insights to spectral features. Here, we use open source planewave DFT packages that employ ultrasoft pseudopotentials to assess the infrared (IR) response of organic compounds and complex co-crystal formulations in the solid state, with and without dispersion corrections. We compare our DFT computed lattice parameters and vibrational modes to experiment and comment on how to improve the agreement between theory and modeling to allow for THz spectroscopy to be used as an analytical probe in complex biologically relevant systems.
Intramolecular alkoxy-carbonylation of hydroxy alkenes promoted by Pd(II) (1990)

Abstract
Improvement of Porphyrin Cellular Delivery and Activity by Conjugation to a Carrier Peptide (2001)

The chemical nuclease metalloporphyrin (manganese(III) porphyrin) can cleave DNA irreversibly and can thus constitute a potential antitumor drug. However, these molecules show low permeability to cell surface membranes. We report here the conjugation of an amphipathic carrier peptide to improve considerably its cellular delivery. The metalloporphyrin-peptide conjugate can be internalized by cells within only 5 min of incubation with a yield as high as 80%. Furthermore, the metalloporphyrin-peptide conjugate is able to cleave in vitro high or low molecular weight DNA to the same extend as metalloporphyrin alone without affecting the sequence-specific cleaving activity of the porphyrin. The conjugate is 100-fold more efficient at inducing tumor cells death than the free metalloporphyrin via a mechanism involving genomic DNA cleavage. The results are promising for further therapeutic applications with antitumor drugs such as metalloporphyrin, and also with other existing drugs by using a carrier peptide system in order to improve the cellular uptake of such molecules.
Direct Vertebral Body Derotation, Thoracoplasty, or Both (2012)

Our results suggest that Th alone, DVBD alone, or both Th and DVBD provide equivalent inclinometer results in patients with mild preoperative rib prominences (≤ 9°), but higher SRS-22 self-image scores are achieved using both Th and DVBD. For larger rib prominences, better inclinometer readings are achieved with Th, although SRS-22 self-image scores are comparable.