gebhart/patrepeval huggingface dataset:
Barriers to Integration of Bioinformatics into Undergraduate Life Sciences Education (2017)

Abstract Bioinformatics, a discipline that combines aspects of biology, statistics, and computer science, is increasingly important for biological research. However, bioinformatics instruction is rarely integrated into life sciences curricula at the undergraduate level. To understand why, the Network for Integrating Bioinformatics into Life Sciences Education (NIBLSE, “nibbles”) recently undertook an extensive survey of life sciences faculty in the United States. The survey responses to open-ended questions about barriers to integration were subjected to keyword analysis. The barrier most frequently reported by the ~1,260 respondents was lack of faculty training. Faculty at associate’s-granting institutions report the least training in bioinformatics and the least integration of bioinformatics into their teaching. Faculty from underrepresented minority groups (URMs) in STEM reported training barriers at a higher rate than others, although the number of URM respondents was small. Interestingly, the cohort of faculty with the most recently awarded PhD degrees reported the most training but were teaching bioinformatics at a lower rate than faculty who earned their degrees in previous decades. Other barriers reported included lack of student interest in bioinformatics; lack of student preparation in mathematics, statistics, and computer science; already overly full curricula; and limited access to resources, including hardware, software, and vetted teaching materials. The results of the survey, the largest to date on bioinformatics education, will guide efforts to further integrate bioinformatics instruction into undergraduate life sciences education.
[ <sup>18</sup> F]FDG PET immunotherapy radiomics signature (iRADIOMICS) predicts response of non-small-cell lung cancer patients treated with pembrolizumab (2020)

Background Immune checkpoint inhibitors have changed the paradigm of cancer treatment; however, non-invasive biomarkers of response are still needed to identify candidates for non-responders. We aimed to investigate whether immunotherapy [18F]FDG PET radiomics signature (iRADIOMICS) predicts response of metastatic non-small-cell lung cancer (NSCLC) patients to pembrolizumab better than the current clinical standards. Patients and methods Thirty patients receiving pembrolizumab were scanned with [18F]FDG PET/CT at baseline, month 1 and 4. Associations of six robust primary tumour radiomics features with overall survival were analysed with Mann-Whitney U-test (MWU), Cox proportional hazards regression analysis, and ROC curve analysis. iRADIOMICS was constructed using univariate and multivariate logistic models of the most promising feature(s). Its predictive power was compared to PD-L1 tumour proportion score (TPS) and iRECIST using ROC curve analysis. Prediction accuracies were assessed with 5-fold cross validation. Results The most predictive were baseline radiomics features, e.g. Small Run Emphasis (MWU, p = 0.001; hazard ratio = 0.46, p = 0.007; AUC = 0.85 (95% CI 0.69-1.00)). Multivariate iRADIOMICS was found superior to the current standards in terms of predictive power and timewise with the following AUC (95% CI) and accuracy (standard deviation): iRADIOMICS (baseline), 0.90 (0.78-1.00), 78% (18%); PD-L1 TPS (baseline), 0.60 (0.37-0.83), 53% (18%); iRECIST (month 1), 0.79 (0.62-0.95), 76% (16%); iRECIST (month 4), 0.86 (0.72-1.00), 76% (17%). Conclusions Multivariate iRADIOMICS was identified as a promising imaging biomarker, which could improve management of metastatic NSCLC patients treated with pembrolizumab. The predicted non-responders could be offered other treatment options to improve their overall survival.
Vitamin K-dependent carboxylase. In vitro inhibitory activity of cyclopentane and cyclohexane-derived analogues of glutamic acid and their conformational study by NMR and molecular dynamics in aqueous solution. (1997)

The conformational analysis of four glutamic acid analogues containing a cyclopentyl or cyclohexyl ring, substituted in position 1 by a Boc-protected amino group and a methyl ester group and in position 3 by a free carboxylate group (6-9), has been carried out in an aqueous environment, by 1H and 13C NMR spectroscopy, and molecular dynamics (MD). These compounds have been shown to be weak competitive inhibitors (Ki approximately 20-65 mM) of the vitamin K-dependent carboxylation of Boc-Glu-OMe in rat liver microsomes independently of their ring size and stereochemical features. However, the cyclic trans isomers have been found more active than the cis ones, and Boc-trans-C5-OMe (9) is the most potent inhibitor in the series (cis and trans isomers are defined by the relative arrangement of the carboxyl functions). Such cyclic glutamyl derivatives may provide valuable informations on the preferred bioactive conformations of synthetic glutamyl substrates at the active site of the carboxylase. In aqueous solution, the Boc-cis- and trans-C6 esters exhibit chair conformations with exclusively equatorial and axial substituent positions, while the Boc-cis- and -trans-C5 compounds may display envelope E or 'twist' T conformations with the substituents in the following positions, equatorial; axial and isoclinal. For each compound, the conformations resulting from NMR and MD data were analyzed and classified according to the dihedral angles chi 1 and chi 2, the distances of functional groups, and the spatial charge distribution involving the free carboxyl group. A reduced number of conformational families were found to be in qualitative agreement with NMR and MD data. These results are discussed in relation with the carboxylase inhibitory activity of the analogues, and a spatial disposition of the glutamyl side chain that could be recognized by the carboxylase is deduced.
Predicting cardiac electrical response to sodium-channel blockade and Brugada syndrome using polygenic risk scores. (2019)

&amp;lt;p&amp;gt;Sodium-channel blockers (SCBs) are associated with arrhythmia, but variability of cardiac electrical response remains unexplained. We sought to identify predictors of ajmaline-induced PR and QRS changes and Type I Brugada syndrome (BrS) electrocardiogram (ECG).&amp;lt;/p&amp;gt;
Improved ion imaging of slowly dried neurons and skin cells by graphene cover in time-of-flight secondary ion mass spectrometry (2019)

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is a powerful tool to obtain both chemical information and spatial distribution of specific molecules of interest on a specimen surface. However, since the focused ion beam requires ultrahigh vacuum conditions for desorption and ionization of analytes, proper specimen preparation, such as drying, freeze-drying, and frozen dehydration, is required for ToF-SIMS analysis. In particular, biological specimens with high moisture content generally have a problem of specimen deformation during the normal drying process for a vacuum environment. In this study, the authors propose a cellular specimen preparation method to improve the ion imaging of cells by reducing the deformation of specimens in ToF-SIMS analysis. When the cells on the slide substrate are completely covered with single-layer graphene, the ToF-SIMS imaging is improved by reduced cell deformation due to slow drying. In addition, the graphene encapsulation also induces a reduction in the yield of secondary ions, thereby suppressing the background ion spectra generated by the unwanted organic residues on the substrate, resulting in the improvement of ToF-SIMS imaging. The authors also found that adding plasma treatment to this sample preparation can further improve ion imaging of cells. After cell dehydration is completed, the covered graphene layer can be peeled off by air-plasma treatment and the unwanted organic residues on the substrate can be removed due to plasma cleaning, thereby much improving ion imaging of cells.
A Comparator-Based Rail Clamp (2015)

A comparator-based rail clamp for handling electrostatic discharge (ESD) events is presented. The new circuit technique allows the use of a time constant that can be much smaller than a traditional RC and inverter-based clamp. The new clamp is more area-efficient and dissipates ESD events with little residual energy. The design is able to support applications with power-ON time slower than 4 μs, is immune to latch-ON, and recovers very quickly if falsely triggered. Experimental results and performance comparisons with the traditional circuit are presented.
Spherical silicon solar cell with reflector cup fabricated by decompression dropping method (2006)

A spherical Si solar cell with a reflector cup was successfully fabricated by a dropping method at decompression state. In the dropping method, melted Si droplets were instilled at decompression state (0.5 × 105 Pa) to reduce crystal growth rate, dominating crystal quality such as dislocation density in crystal grains. Spherical Si solar cells were fabricated using the spherical Si crystals with a diameter of 1 mm and then mounted on a reflector cup. The current-voltage measurement of the solar cell shows an energy conversion efficiency of 11.1% (short-circuit current density (Jsc): 24.7 mA·cm−2, open-circuit voltage: 601 mV, fill factor: 74.6%). Minority carrier diffusion length determined by surface photovoltage method was 98 μm. This value can be enhanced by the improvement of crystal quality of spherical Si crystals. These results demonstrate that spherical Si crystals fabricated by the dropping method has a great potential for substrate material of high-efficiency and low-cost solar cells.
Circulating tumour DNA from the cerebrospinal fluid allows the characterisation and monitoring of medulloblastoma (2020)

The molecular characterisation of medulloblastoma, the most common paediatric brain tumour, is crucial for the correct management and treatment of this heterogenous disease. However, insufficient tissue sample, the presence of tumour heterogeneity, or disseminated disease can challenge its diagnosis and monitoring. Here, we report that the cerebrospinal fluid (CSF) circulating tumour DNA (ctDNA) recapitulates the genomic alterations of the tumour and facilitates subgrouping and risk stratification, providing valuable information about diagnosis and prognosis. CSF ctDNA also characterises the intra-tumour genomic heterogeneity identifying small subclones. ctDNA is abundant in the CSF but barely present in plasma and longitudinal analysis of CSF ctDNA allows the study of minimal residual disease, genomic evolution and the characterisation of tumours at recurrence. Ultimately, CSF ctDNA analysis could facilitate the clinical management of medulloblastoma patients and help the design of tailored therapeutic strategies, increasing treatment efficacy while reducing excessive treatment to prevent long-term secondary effects.
Ultra-high gain in an Yb3+-doped dielectric waveguide (2011)

Thanks to high dopant concentration, large transition cross-sections, and strong light confinement, modal gain of ~1000 dB/cm, comparable to semiconductor optical amplifiers, is demonstrated in a large-refractive-index-contrast KGd0.535Yb0.475(WO4)2 channel waveguide on a KY(WO4)2 substrate.
Supplementary Figures S1-S16 from Sex-Biased T-cell Exhaustion Drives Differential Immune Responses in Glioblastoma (2023)

&lt;p&gt;Supplementary Fig. S1. Immune cell-dependent survival differences between males and females in murine glioblastoma models. Supplementary Fig. S2. Mouse syngeneic GBM cell lines do not contain a Y chromosome. Supplementary Fig. S3. Frequencies of tumor-infiltrating immune cells in SB28 model. Supplementary Fig. S4. Sex difference in survival in SB28-OVA model and GL261 model. Supplementary Fig. S5. No sex difference in T cells was observed at an earlier time point. Supplementary Fig. S6. Male T cells are more exhausted in the GL261 model. Supplementary Fig. S7. Phenotype of T cells in the periphery does not replicate the sex differences shown in tumor-infiltrating T cells. Supplementary Fig. S8. Frequencies of exhausted T cell subsets. Supplementary Fig. S9. PD1 blockade enhanced immune responses Supplementary Fig. S10. No significant difference in the immune cell composition of bone marrow chimera mice before tumor implantation. Supplementary Fig. S11. Male and female CD8+ T cells in mixed bone marrow chimera model. Supplementary Fig. S12. Phenotyping tumor-infiltrating CD8+ T cell from GBM patient tumors. Supplementary Fig. S13. scRNA-seq analysis of tumor-infiltrating CD8+ T cells from GBM patients. Supplementary Fig. S14. mRNA expression level of transcription factors in human in vitro exhausted T cells. Supplementary Fig. S15. Expression level of X chromosome inactivation (XCI) genes in exhausted T cells. Supplementary Fig. S16. Inhibition of UTX abrogates sex differences in T cell exhaustion.&lt;/p&gt;
Reducing Modal Noise in Short-Range Radio over Multimode Fibre Links (2010)

Reducing gain fluctuations in Short Range Radio over Multimode Fiber Links requires Central Launch. Furthermore, the quality of today’s optical connectors gives importance to the combined effect of finite detecting area and Laser frequency chirp.
Synthesis of Novel <scp>d</scp>-2‘-Deoxy-2‘- <i>C</i>-difluoromethylene-4‘-thiocytidine as a Potential Antitumor Agent (2002)

[reaction: see text] 2'-Deoxy-2'-C-difluoromethylene-4'-thiocytidine (4) as a potential antitumor agent was synthesized starting from L-xylose via 2-deoxy-2-C-difluoromethylene-4-thiosugar as a key intermediate. An elimination product, 8, was always formed as the major product during removal of the protecting groups under acidic or basic conditions. However, utilizing neutral reaction conditions to remove the protecting groups afforded the desired product 4 exclusively.
Mix Design and Benefit Evaluation of High Solar Reflectance Concrete for Pavements (2007)

The use of cool paving materials, or cool pavements, has been identified as one strategy that can help mitigate the urban “heat island” effect. One method of creating a cool pavement is to increase the solar reflectance, or albedo, of its surface. This increase can be achieved by many existing paving technologies. This study explores alternative ways of creating high-albedo concrete for use in pavement applications. The key approach is to make concrete whiter by replacing cement with whiter constituents. Fly ash and slag are used as the main constituents because they are environmentally friendly, readily available, and already familiar to the concrete industry. Compared with a conventional concrete mix, concrete mixes containing fly ash have lower albedo, whereas concrete mixes containing slag have higher albedo. Of all mixes tested, the mix with 70% slag as cement replacement achieves the highest albedo of 0.582, which is 71% higher than the conventional mix. It also has better compressive strength as tested at 7 and 28 days and modulus of rupture as tested at 7 days. The production of high solar reflectance concrete consumes 43.5% less energy and results in less emission of pollutants and greenhouse gases (by 20% to 60%). Furthermore, the analysis of some urban cities shows that the implementation of this high solar reflectance concrete could increase the city albedo by 0.02 to 0.07. This amount of albedo modification has the potential to benefit economics and the environment in many ways, ranging from decreasing energy demand to improving air quality.
Establishment of a novel pork kidney lavage method and detection of heavy metals and antibiotics (2022)

The effectiveness and feasibility of a pork kidney lavage method to remove heavy metals and antibiotics from fresh pork kidney were investigated. This work provides a basis for the research and development of contaminant-free pork kidney foods. A comparative study was performed on pork kidneys with traditional treatment versus lavage treatment. The contents of Cu, Pb and Hg, 18 sulfonamides, 15 quinolones, ampicillin and cefalexin were detected by FAAS, GF-AAS, AFS and LC-MS/MS. The detection results of heavy metals and antibiotics showed that the content of Cu in pork kidney after lavage was significantly reduced, and antibiotics such as sulfachlorpyridazine and enrofloxacin were not detected. Therefore, lavage is an effective method to remove toxins from fresh pork kidney and can remove heavy metals and antibiotics to the maximum extent, providing a basic guarantee for the production of contaminant-free pork kidney foods.
N-Phenylpyridine-3-Carboxamide and 6-Acetyl-1H-Indazole Inhibit the RNA Replication Step of the Dengue Virus Life Cycle (2023)

Dengue virus (DENV) is a <i>Flavivirus</i> that causes the most prevalent arthropod-borne viral disease. Clinical manifestation of DENV infection ranges from asymptomatic to severe symptoms that can lead to death. Unfortunately, no antiviral treatments against DENV are currently available. In order to identify novel DENV inhibitors, we screened a library of 1,604 chemically diversified fragment-based compounds using DENV reporter viruses that allowed quantification of viral replication in infected cells. Following a validation screening, the two best inhibitor candidates were N-phenylpyridine-3-carboxamide (NPP3C) and 6-acetyl-1H-indazole (6A1HI). The half maximal effective concentration of NPP3C and 6A1H1 against DENV were 7.1 μM and 6.5 μM, respectively. 6A1H1 decreased infectious DENV particle production up to 1,000-fold without any cytotoxicity at the used concentrations. While 6A1HI was DENV-specific, NPP3C also inhibited the replication of other flaviviruses such as West Nile virus and Zika virus. Structure-activity relationship (SAR) studies with 151 analogues revealed key structural elements of NPP3C and 6A1HI required for their antiviral activity. Time-of-drug-addition experiments identified a postentry step as a target of these compounds. Consistently, using a DENV subgenomic replicon, we demonstrated that these compounds specifically impede the viral RNA replication step and exhibit a high genetic barrier-to-resistance. In contrast, viral RNA translation and the <i>de novo</i> biogenesis of DENV replication organelles were not affected. Overall, our data unveil NPP3C and 6A1H1 as novel DENV inhibitors. The information revealed by our SAR studies will help chemically optimize NPP3C and 6A1H1 in order to improve their anti-flaviviral potency and to challenge them in <i>in vivo</i> models.
Interleukin 4 induces membrane Thy-1 expression on normal murine B cells. (1988)

Thy-1, a cell-surface glycoprotein of undetermined function, is expressed in relatively large amounts on mouse thymocytes, peripheral T cells, and neurons. It is widely used as a marker to distinguish peripheral T cells from B cells in mice. We show here that, in five distinct mouse strains, recombinant interleukin 4 (IL-4/B-cell stimulatory factor 1) strikingly induces membrane expression of Thy-1 on the vast majority of lipopolysaccharide (LPS)-stimulated normal murine B cells. Thy-1+ B cells are precursors for immunoglobulin-secreting cells. RNA blot analysis indicates that B cells express a Thy-1 mRNA of 1.8 kilobases, the same size as that found in T cells. Cell mixing experiments show that only cells derived from Thy-1.2+ donors express Thy-1.2, indicating that B cells expressing Thy-1 have not passively absorbed the glycoprotein from another cell source. Recombinant interferon-gamma inhibits Thy-1 induction by B cells stimulated with LPS and IL-4. Thy-1 is also induced on B cells that have been stimulated as a result of the specific activation of an IL-4-producing T-helper clone. Anti-IL-4 monoclonal antibody inhibits the induction of B-cell Thy-1 in this T-cell-B-cell interaction.
Reliability and concurrent validity of instrumented balance error scoring system using a portable force plate system (2015)

Although the instrumented BESS may appear to demonstrate concurrent validity against the original BESS, instrumentation did not improve its reliability. Future research should examine if the instrumented BESS demonstrates validity against laboratory level force plates and if it is able to overcome the ceiling effect reported for the clinical BESS test.
Mth1 regulates the interaction between the Rgt1 repressor and the Ssn6-Tup1 corepressor complex by modulating PKA-dependent phosphorylation of Rgt1 (2013)

Glucose uptake, the first, rate-limiting step of its utilization, is facilitated by glucose transporters. Expression of several glucose transporter (HXT) genes in yeast is repressed by the Rgt1 repressor, which recruits the glucose-responsive transcription factor Mth1 and the general corepressor complex Ssn6-Tup1 in the absence of glucose; however, it is derepressed when Mth1 is inactivated by glucose. Here we show that Ssn6-Tup1 interferes with the DNA-binding ability of Rgt1 in the absence of Mth1 and that the Rgt1 function abrogated by Ssn6 overexpression is restored by co-overexpression of Mth1. Thus Mth1 likely regulates Rgt1 function not by modulating its DNA-binding activity directly but by functionally antagonizing Ssn6-Tup1. Mth1 does so by acting as a scaffold-like protein to recruit Ssn6-Tup1 to Rgt1. Supporting evidence shows that Mth1 blocks the protein kinase A-dependent phosphorylation of Rgt1 that impairs the ability of Rgt1 to interact with Ssn6-Tup1. Of note, Rgt1 can bind DNA in the absence of Ssn6-Tup1 but does not inhibit transcription, suggesting that dissociation of Rgt1 from Ssn6-Tup1, but not from DNA, is necessary and sufficient for the expression of its target genes. Taken together, these findings show that Mth1 is a transcriptional corepressor that facilitates the recruitment of Ssn6-Tup1 by Rgt1.
Ion-induced discrete charging of immobilized water-soluble gold nanoclusters (2002)

Hydrophilic gold nanoclusters were immobilized onto monolayer-modified gold electrodes and PF6-(-)induced rectification and stepwise capacitance charging was studied in aqueous supporting electrolyte by cyclic voltammetry and ac voltammetry.
Improve vertical sweet-spot of 3-D sound system by loudspeaker arrays (2013)

Recently, we have proposed a 3-D sound system using horizontal arrange loudspeakers by combine the effect of HRTF and the amplitude panning method. In that system, loudspeakers are set at the height of subject's ear level and its sweet-spot is limited by the height of loudspeakers. When listener's ear level is different with loudspeakers, it will cause difficulty of sound localization or breakdown of sound localization. However, it is difficult to adjust properly both the height of loudspeakers and subject's ear level every time. In this paper, we aimed to improve the robustness of the 3-D sound system using vertical loudspeakers array. As a result of experiments, we verify that the loudspeaker arrays can improve the robustness of the 3-D sound system.
Vanadium-Doped Ni/YSZ Anode Functional Layers for Solid Oxide Fuel Cells Produced via Magnetron Sputtering (2023)

The electrode performance of solid oxide fuel cells (SOFCs) strongly depends on their microstructural characteristics, such as the porosity, percolated paths of ionically and electronically conductive phases and in particular, the grain size. Deploying alternative manufacturing techniques, such as magnetron sputtering, that deposits nanostructured materials results in finer particle sizes and thus, increases the quantity of triple-phase boundaries in the anode functional layer (AFL) for SOFCs. Nanostructured NiO-YSZ thin films have been previously produced by reactive pulsed DC magnetron co-sputtering of metallic targets of zirconium-yttrium and nickel, defining the optimal deposition parameters to create state-of-the-art AFLs. Based on recent studies 1–3, the future of oxide-based anode materials for SOFCs will greatly focus on advancing the electrocatalyst through alternative non-precious metal doping and increasing the cell performance by tailoring the microstructure of the AFL. Therefore, in this study, vanadium oxides were doped into SOFC anodes using different concentrations to study their influence on the structural and morphological properties of magnetron-sputtered AFLs.