gebhart/patrepeval huggingface dataset:
Management of patients with diabetes and heart failure with reduced ejection fraction: An international comparison (2018)

In both the United States and Asia, opportunities for improvement in the use of evidence-based therapies exist for patients with both diabetes and HFrEF. Effective tools to guide medication choices for these complex, high-risk patients could have substantial impact on quality and outcomes.
Low-frequency propagation and noise in the intertidal zone (2016)

Measurements of ambient noise and short-range propagation (&amp;lt;2m) were made in the intertidal zone with water depths ranging from 50 to 80 cm using vector sensors. The sites selected for the measurements were known nesting areas for plainfin midshipman (Porichthys notatus). Males of this species produce continuous acoustic advertisement calls with fundamental frequencies in the 70 to 100 Hz range. The temporal and spectral structure of these calls must convey information regarding the source’s range, direction, and/or fitness over the maximum detectable range in a complex environment. Both fundamental and harmonic components appear to be above a rapid low-frequency increase in the noise floor due to local wave motion and below the frequency range of several observed noise transients at times with modest wind speeds (&amp;lt;5 mph) and small wave heights (&amp;lt;20cm). There is little evidence of significant propagation differences between specific frequencies within the band of interest.
Is there a single vibrato waveform (1988)

High-fidelity singing synthesis requires careful consideration of the properties and character of natural vibrato. In many synthesis methods, a single vibrato waveform is derived and applied equally to all of the partials of the synthesized tone. The research reported here tests the validity of this linear treatment of vibrato using an analysis/synthesis procedure. The singing tone /ah/ is analyzed for bass, tenor, alto, and soprano voices, providing time-variant measurements of amplitude, frequency, and phase for each of the partials. The tones are reconstructed using an additive synthesis procedure. The importance of vibrato waveform similarities and differences between partials is evaluated by resynthesis of the singing tones from modified analysis data. The modifications include the use of the fundamental partial's vibrato waveform for all of the partials, the use of sinusoidal vibrato for all the partials, the elimination of amplitude variations for each partial, and various combinations. The analysis data and examples of the resynthesis will be presented. [Work supported, in part, by an NSF Graduate Fellowship.]
Use of Non‐Normalized, Non‐Amplified cDNA for 454‐Based RNA Sequencing of Fleshy Melon Fruit (2011)

The melon ( Cucumis melo L.) fruit is an important crop and model system for the genomic study of both fleshy fruit development and the Cucurbitaceae family. To obtain an accurate representation of the melon fruit transcriptome based on expressed sequence tag (EST) abundance in 454‐pyrosequencing data, we prepared double‐stranded complementary DNA (cDNA) of melon without the usual amplification and normalization steps. A purification step was also included to eliminate small fragments. Complementary DNAs were obtained from 14 individual fruit libraries derived from two genotypes, separated into flesh and peel tissues, and sampled throughout fruit development. Pyrosequencing was performed using Genome Sequencer FLX (GS FLX) technology, resulting in 1,215,359 reads, with mean length of &gt;200 nucleotides. The global digital expression data was validated by comparative reverse transcription quantitative real‐time polymerase chain reaction (RT‐qPCR) of 40 selected genes and expression patterns were similar for the two methods. The results indicate that high‐quality, nonbiased cDNA for next‐generation sequencing can be prepared from mature, fleshy fruit, which are notorious for difficulties in ribonucleic acid (RNA) preparation.
Enrichment and Clonal Culture of Hepatic Stem/Progenitor Cells During Mouse Liver Development (2012)

Liver regenerates after hepatectomy or chemical-induced injury. In contrast to cells in other tissues that can regenerate, mature cells (hepatocytes), but not undifferentiated stem cells, are mainly responsible for acute liver regeneration. Liver stem cells take part in liver regeneration in some forms of chronic liver injury, when the proliferative ability of differentiated hepatocytes is impaired. During liver development, both hepatocytes and cholangiocytes are differentiated from common precursor cells, called hepatoblasts. By combining fluorescence-activated cell sorting (FACS) and an in vitro clonal culture system for stem/progenitor cells, we established a method to isolate stem/progenitor cells prospectively from mouse fetal and adult livers. FACS clone-sorted single CD45(-)Ter119(-)c-kit(-)CD13(+)CD133(+) cells (from fetal mid-gestational livers) or CD45(-)Ter119(-)c-kit(-)Sca1(-)CD13(+)CD49f(+)CD133(+) cells (from adult livers) can form a colony containing both albumin-positive hepatocytes and cytokeratin 19-positive bile ductal cells, indicating that these cells have the characters of liver stem/progenitor cells (proliferative capability and bipotency for hepatic and for biliary epithelial differentiation). These cells can maintain these capabilities for several months in culture.
Modeling and Prediction of Frac-Pack Tool Erosion in Multizone Wells (2014)

Reservoir conditions in attractive deepwater wells are leading operators to request increasing frac pump rates and proppant volumes in order to achieve effective frac packs. Additionally, a long payzone can be difficult to stimulate and complete in a single interval due to multilayer formations with varying properties. Therefore, the best completion practice is to isolate the payzone into multiple zones of production. As a result, the frac pack service equipment used to treat multiple zones is exposed to an accumulative amount of high rate erosive flow. The tools which deliver these stimulations must be qualified using testing procedures which replicate actual job conditions, as closely as possible, to ensure the integrity of these tools when deployed in these challenging environments. High stimulation rates and large slurry volumes which must be replicated in a testing environment require an investment in assets and logistics on the order of that required for an actual deployment. Therefore, testing parameters must be selected based on those anticipated in the completion for which the tools are being qualified. Modeling and analysis techniques have advanced resulting in improved erosion prediction and optimized frac port geometry and materials. Full scale designs have been thoroughly tested following analysis. The results and correlations of analysis and test results will be discussed. The analysis and testing methods of erosion resistant design and materials leads to more efficient launch of new technology to meet sand control needs in challenging deepwater multizone wells.
Structural Elucidation of Chalcone Reductase and Implications for Deoxychalcone Biosynthesis (2005)

4,2',4',6'-Tetrahydroxychalcone (chalcone) and 4,2',4'-trihydroxychalcone (deoxychalcone) serve as precursors of ecologically important flavonoids and isoflavonoids. Deoxychalcone formation depends on chalcone synthase and chalcone reductase; however, the identity of the chalcone reductase substrate out of the possible substrates formed during the multistep reaction catalyzed by chalcone synthase remains experimentally elusive. We report here the three-dimensional structure of alfalfa chalcone reductase bound to the NADP+ cofactor and propose the identity and binding mode of its substrate, namely the non-aromatized coumaryl-trione intermediate of the chalcone synthase-catalyzed cyclization of the fully extended coumaryl-tetraketide thioester intermediate. In the absence of a ternary complex, the quality of the refined NADP+-bound chalcone reductase structure serves as a template for computer-assisted docking to evaluate the likelihood of possible substrates. Interestingly, chalcone reductase adopts the three-dimensional structure of the aldo/keto reductase superfamily. The aldo/keto reductase fold is structurally distinct from all known ketoreductases of fatty acid biosynthesis, which instead belong to the short-chain dehydrogenase/reductase superfamily. The results presented here provide structural support for convergent functional evolution of these two ketoreductases that share similar roles in the biosynthesis of fatty acids/polyketides. In addition, the chalcone reductase structure represents the first protein structure of a member of the aldo/ketoreductase 4 family. Therefore, the chalcone reductase structure serves as a template for the homology modeling of other aldo/keto-reductase 4 family members, including the reductase involved in morphine biosynthesis, namely codeinone reductase.
Prepare for the Future: Dissecting the Spike to Seek Broadly Neutralizing Antibodies and Universal Vaccine for Pandemic Coronaviruses (2020)

Learning from the lengthy fight against HIV-1, influenza, and Ebola virus infection, broadly neutralizing antibodies (bnAbs), directed at conserved regions of surface proteins crucial to virus entry (Env, hemagglutinin, and GP, respectively), are an essential resource for passive as well as active immunization. Rare in their emergence and antigen recognition mode, bnAbs are active toward a large set of different viral strains. Isolation, characterization and production of bnAbs lead to their possible use in passive immunotherapy and form the basis for an educated effort in the development of vaccines for universal coverage. SARS-CoV-2-specific antibodies targeting the spike receptor binding domain (RBD) may lead to antibody dependent enhancement (ADE) of infection, possibly hampering the field of vaccine development. This perspective points to the identification of conserved regions in the spike of SARS-CoV-2, SARS-CoV, and MERS-CoV through investigation, dissection and recombinant production of isolated moieties. These spike moieties should be capable of independent folding and allow the detection as well as the elicitation of bnAbs, thus setting the basis for an effective passive immunotherapy and the development of a universal vaccine against human epidemic coronaviruses (HCoVs). SARS, MERS and, most of all, COVID-19 demonstrate that humanity is the target of HCoV, preparedness for future hits is thus no longer an option.
<title>Optical properties of KDP crystals grown at high growth rates</title> (1991)

Comparative analysis of main optical characteristics of KDP crystals grown by traditional technique at growth rates up to 1 mm/day and by rapid growth technique at growth rates ranging from 15 to 40 mm/day is carried out. The results on anomalous biaxiality absorption ard scattering of light effective nonlinear susceptibility and bulk laser damage threshold of crystals are given. It is shown that the increase of the crystal growth rate by more than one order does not deteriorate the crystal optical quality.
Biomimetic and Biologically Compliant Soft Architectures via 3D and 4D Assembly Methods: A Perspective (2022)

Recent progress in soft material chemistry and enabling methods of 3D and 4D fabrication-emerging programmable material designs and associated assembly methods for the construction of complex functional structures-is highlighted. The underlying advances in this science allow the creation of soft material architectures with properties and shapes that programmably vary with time. The ability to control composition from the molecular to the macroscale is highlighted-most notably through examples that focus on biomimetic and biologically compliant soft materials. Such advances, when coupled with the ability to program material structure and properties across multiple scales via microfabrication, 3D printing, or other assembly techniques, give rise to responsive (4D) architectures. The challenges and prospects for progress in this emerging field in terms of its capacities for integrating chemistry, form, and function are described in the context of exemplary soft material systems demonstrating important but heretofore difficult-to-realize biomimetic and biologically compliant behaviors.
Alternative promoter and GATA5 transcripts in mouse (2009)

GATA5 is a member of the GATA zinc finger transcription factor family involved in tissue-specific transcriptional regulation during cell differentiation and embryogenesis. Previous reports indicate that null mutation of the zebrafish GATA5 gene results in embryonic lethality, whereas deletion of exon 1 from the mouse GATA5 gene causes only derangement of female urogenital development. Here, we have identified an alternate promoter within intron 1 of the mouse GATA5 gene that transcribes a 2.5-kb mRNA that lacks exon 1 entirely but includes 82 bp from intron 1 and all of exons 2-6. The alternative promoter was active during transient transfection in cultured airway myocytes and bronchial epithelial cells, and it drove reporter gene expression in gastric epithelial cells in transgenic mice. The 2.5-kb alternative transcript encodes an NH(2)-terminally truncated "short GATA5" comprising aa 226-404 with a single zinc finger, which retains ability to transactivate the atrial natriuretic factor promoter (albeit less efficiently than full-length GATA5). Another new GATA5 transcript contains all of exons 1-5 and the 5' portion of exon 6 but lacks the terminal 1143 bp of the 3'-untranslated region from exon 6. These findings extend current understanding of the tissue distribution of GATA5 expression and suggests that GATA5 expression and function are more complex than previously appreciated.
Vaccine-induced, but not natural immunity, against the Streptococcal Inhibitor of Complement protects against invasive disease (2020)

Abstract Highly pathogenic emm1 Streptococcus pyogenes strains secrete the multidomain Streptococcal inhibitor of complement (SIC) that binds and inactivates components of the innate immune response. We aimed to determine if naturally occurring or vaccine-induced antibodies to SIC are protective against invasive S. pyogenes infection. Immunisation with full length SIC protected mice against systemic bacterial dissemination following intranasal or intramuscular infection with emm1 S. pyogenes. Vaccine-induced rabbit anti-SIC antibodies, but not naturally occurring human anti-SIC antibodies, enhanced bacterial clearance in an ex vivo whole blood assay. SIC vaccination of both mice and rabbits resulted in antibody recognition of all domains of SIC, whereas naturally occurring human anti-SIC antibodies recognised the proline-rich region of SIC only. We therefore propose a model whereby natural infection with S. pyogenes generates non-protective antibodies against the proline-rich region of SIC, while vaccination with full length SIC permits development of protective antibodies against all SIC domains.
Reducing Pull-In Voltage by Adjusting Gap Shape in Electrostatically Actuated Cantilever and Fixed-Fixed Beams (2010)

A gap with variable geometry is presented for both cantilever beam and fixed-fixed beam actuators as a method to reduce the pull-in voltage while maintaining a required displacement. The method is applicable to beams oriented either in a plane parallel to or perpendicular to a substrate, but is most suitable for vertically oriented (lateral) beams fabricated with a high aspect ratio process where variable gap geometry can be implemented directly in the layout. Finite element simulations are used to determine the pull-in voltages of these modified structures. The simulator is verified against theoretical pull-in voltage equations as well as previously published finite element simulations. By simply varying the gap in a linear fashion the pull-in voltage can be reduced by 37.2% in the cantilever beam case and 29.6% in the fixed-fixed beam case over a structure with a constant gap. This can be reduced a further 4.8% by using a polynomial gap shape (n = 4/3) for the cantilever beam and 1.2% for the fixed-fixed beam by flattening the bottom of the linearly varying gap.
Long-Term Outcomes in Patients With BRAF V600–Mutant Metastatic Melanoma Who Received Dabrafenib Combined With Trametinib (2017)

Purpose To report 5-year landmark analysis efficacy and safety outcomes in patients with BRAF V600-mutant metastatic melanoma (MM) who received BRAF inhibitor dabrafenib (D) and MEK inhibitor trametinib (T) combination therapy versus D monotherapy in the randomized phase II BRF113220 study part C. Patients and Methods BRAF inhibitor-naive patients with BRAF V600-mutant MM were randomly assigned 1:1:1 to receive D 150 mg twice a day, D 150 mg twice a day plus T 1 mg once daily, or D 150 mg twice a day plus T 2 mg once daily (D + T 150/2). Patients who received D monotherapy could cross over to D + T 150/2 postprogression. Efficacy and safety were analyzed 4 and 5 years after initiation in patients with ≥ 5 years of follow-up. Results As of October 13, 2016, 18 patients who received D + T 150/2 remained in the study (13 [24%] of 54 enrolled at this dose plus five [11%] of 45 initially administered D who crossed over to D + T). With D + T 150/2, overall survival (OS; 4 years, 30%; 5 years, 28%) and progression-free survival (4 and 5 years, both 13%) appeared to stabilize with extended follow-up. Increased OS was observed in patients who received D + T with baseline normal lactate dehydrogenase (5 years, 45%) and normal lactate dehydrogenase with fewer than three organ sites with metastasis (5 years, 51%). With extended follow-up, one additional patient who received D + T 150/2 improved from a partial to a complete response. No new safety signals were observed. Conclusion This 5-year analysis represents the longest follow-up to date with BRAF + MEK inhibitor combination therapy in BRAF V600-mutant MM. Consistent with trends observed in landmark analyses with shorter follow-up, this therapy elicits durable plateaus of long-term OS and progression-free survival that last ≥ 5 years in some patients with MM.
A New Slice-based Concept for 3D Paper Structure Analysis Applied to Spatial Coating Layer Formation (2005)

This paper introduces a new concept for digitizing the three dimensional paper structure, based on a fully automated microtomy process and light microscopy. The microscope can be moved in all three directions of space with high accuracy in order to be able to digitize large samples with high spatial resolution. All components are controlled by a PC interface which enables an automated digitization process. The literature concerning 3D analysis of paper structure is reviewed. Non destructive and destructive techniques are compared. Image analysis algorithms for creation of a detailed digital representation are described. This digital data set is analyzed, to derive characteristics of the paper structure. As a first example of possible applications the analysis of the 3D coating layer formation is presented. The coating layer is detected by means of image analysis based on a 3D color segmentation concept. Initial experiments on analyzing coated paper samples prove the applicability of the concept. The correctness of the implemented sample digitization process and following image analysis was validated.
Destruction of a first-order smectic-A→smectic-C*phase transition by dimensional crossover in free-standing films (1993)

Shifting and destruction of phase transitions due to the finite thickness of free-standing smectic films are examined. The behavior of smectic films is studied as a function of the temperature and the thickness in a material showing a first-order smectic-A (Sm-A)\ensuremath{\rightarrow}smectic-${\mathit{C}}^{\mathrm{*}}$ (Sm-${\mathit{C}}^{\mathrm{*}}$) bulk phase transition. Measurements of the optical reflectivity and direct observations in an inverted polarizing microscope reveal that the first-order phase transition between Sm-A- and Sm-${\mathit{C}}^{\mathrm{*}}$-like structures takes place in films that are thick enough (N&gt;${\mathit{N}}_{\mathit{c}}$=90). In thin films (N${\mathit{N}}_{\mathit{c}}$) this transition disappears. For N\ensuremath{\approxeq}${\mathit{N}}_{\mathit{c}}$, a critical behavior is detected. A theoretical scheme for interpretation of phase transitions in smectic films is proposed and on its basis a conjecture on tension-induced phase transitions is formulated.
Performance Analysis of Cooperative Systems With Unreliable Backhauls and Selection Combining (2016)

In this paper, a cooperative wireless system with unreliable wireless backhaul connections is investigated. To increase the throughput and maximize the receiver signal-to-noise ratio (SNR), a selection combining (SC) protocol is employed. Cooperative transmitters are connected to the control unit (CU) via independent but unreliable wireless backhaul connections. Simultaneously taking into account the reliability of each backhaul and different fading conditions of Nakagami-m fading channels, the statistical properties of the effective SNR (e-SNR) at the receiver are investigated. Closed-form expressions are derived for several performance metrics, including the outage probability, average spectral efficiency (ASE), and average symbol error rate (ASER). The effects of backhaul reliability on these performance metrics are also investigated. The scaling relationship between the convergence behavior of these performance metrics and the conventional diversity gain is also analytically investigated in the asymptotic high-SNR regime. Monte Carlo simulations are conducted to verify the derived impact of backhaul reliability on the performance.
A novel combination of serum microRNAs for the detection of early gastric cancer (2021)

A novel combination of four serum miRNAs could be a useful non-invasive diagnostic biomarker to detect EGC with high accuracy. A multicenter prospective study is ongoing to confirm the present observations.
Amelioration of tamoxifen-induced liver injury in rats by grape seed extract, black seed extract and curcumin. (2010)

Liver injury was induced in female rats using tamoxifen (TAM). Grape seeds (Vitis vinifera) extract (GSE), black seed (Nigella sativa) extract (NSE), curcumin (CUR) or silymarin (SYL) were orally administered to TAM-intoxicated rats. Liver histopathology of TAM-intoxicated:rats showed pathological changes. TAM-intoxication elicited declines in liver antioxidant enzymes levels (glutathione peroxidase, glutathione reductase, superoxide dismutase and catalase), reduced glutathione (GSH) and GSH/GSSG ratio plus the hepatic elevations in lipid peroxides, oxidized glutathione (GSSG), tumor necrosis factor-alpha (TNF-alpha) and serum liver enzymes; alanine transaminase, aspartate transaminase, alkaline phosphatase, lactate dehydrogenase and gamma glutamyl transferase levels. Oral intake of NSE, GSE, CUR or SYL to TAM-intoxicated rats, attenuated histopathological changes and corrected all parameters mentioned above. Improvements were prominent in case of NSE (similarly SYL) > CUR > GSE. Data indicated that NSE, GSE or CUR act as free radicals scavengers and protect TAM-induced liver injury in rats.